Dear All, I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don't know how to do the "apply_cif_link' for the extensions such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don't know how to do the "apply_cif_link' for the extensions such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated.
Search in the mon_lib_list.cif file for "data_link_ALPHA" and "data_link_BETA" to find the links you need, then specify them in additional apply_cif_link blocks, one for each link. The command phenix.where_mon_lib_list_cif will give you the location of the mon_lib_list.cif file. Let me know if you cannot find all the links you need. Reports about the links should appear in the phenix.refine log. You can check in the .geo file if all restraints were built correctly. Ralf
you can try elbow to make library for the 'new monomers'. Zhou, Tongqing (NIH/VRC) [E] wrote:
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
Thanks,
Tongqing
*Tongqing Zhou, Ph.D. *
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
*/******************************************************************/*//
*/The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives./*
*/******************************************************************/*
------------------------------------------------------------------------
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Hi Tongqing, Make a sugars.edits ascii file with links like the following between two manoses refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name O2 and chain A and resname MAN and resseq 1490 atom_selection_2 = name C1 and chain A and resname MAN and resseq 1491 distance_ideal = 1.439000 sigma = 0.020 } } and then include this file when running phenix.refine in the command mode, e.g. phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \ refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \ strategy=individual_sites+individual_adp simulated_annealing=true \ main.number_of_macro_cycles=10 Best regards, Blaine ********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877 ________________________________________ From: [email protected] [[email protected]] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [[email protected]] Sent: Tuesday, November 10, 2009 12:12 PM To: '[email protected]' Subject: [phenixbb] Glycan refinement Dear All, I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
Hi Blaine, That might not work correctly. You may get the stereochemistry of the linkage incorrect if you use just a bond distance restraint. You should use linkage types like BETA1-4, or ALPHA1-6, depending on the type of the linkage. And as I have mentioned in the email before, you should also call your beta mannose BMA, and alpha mannose MAN (see the references I mentioned in that email). So something like this would be my guess: apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 902 residue_selection_2 = chain A and resname BMA and resid 903 } apply_cif_link { data_link = ALPHA1-6 residue_selection_1 = chain A and resname BMA and resid 903 residue_selection_2 = chain A and resname MAN and resid 904 } Please correct me if I am wrong. Engin On 11/10/09 11:23 AM, Mooers, Blaine H.M. (HSC) wrote:
Hi Tongqing,
Make a sugars.edits ascii file with links like the following between two manoses
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name O2 and chain A and resname MAN and resseq 1490 atom_selection_2 = name C1 and chain A and resname MAN and resseq 1491 distance_ideal = 1.439000 sigma = 0.020 } }
and then include this file when running phenix.refine in the command mode, e.g.
phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \ refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \ strategy=individual_sites+individual_adp simulated_annealing=true \ main.number_of_macro_cycles=10
Best regards,
Blaine
********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center
Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419
office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
________________________________________ From: [email protected] [[email protected]] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [[email protected]] Sent: Tuesday, November 10, 2009 12:12 PM To: '[email protected]' Subject: [phenixbb] Glycan refinement
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
Thanks,
Tongqing
Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
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-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Engin, Blaine and all, Thanks for the suggestions. The data_links of BETA1-4, ALPHA1-6 are exactly the terms I am looking for. Yes, the refinement of glycans is somewhat tricky with the complexity of sugars links. The good thing is that PDB.org is checking the pdbs for bad glycans before final deposit. Best regards, Tongqing -----Original Message----- From: Engin Ozkan [mailto:[email protected]] Sent: Tuesday, November 10, 2009 2:36 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Glycan refinement Hi Blaine, That might not work correctly. You may get the stereochemistry of the linkage incorrect if you use just a bond distance restraint. You should use linkage types like BETA1-4, or ALPHA1-6, depending on the type of the linkage. And as I have mentioned in the email before, you should also call your beta mannose BMA, and alpha mannose MAN (see the references I mentioned in that email). So something like this would be my guess: apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 902 residue_selection_2 = chain A and resname BMA and resid 903 } apply_cif_link { data_link = ALPHA1-6 residue_selection_1 = chain A and resname BMA and resid 903 residue_selection_2 = chain A and resname MAN and resid 904 } Please correct me if I am wrong. Engin On 11/10/09 11:23 AM, Mooers, Blaine H.M. (HSC) wrote:
Hi Tongqing,
Make a sugars.edits ascii file with links like the following between two manoses
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name O2 and chain A and resname MAN and resseq 1490 atom_selection_2 = name C1 and chain A and resname MAN and resseq 1491 distance_ideal = 1.439000 sigma = 0.020 } }
and then include this file when running phenix.refine in the command mode, e.g.
phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \ refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \ strategy=individual_sites+individual_adp simulated_annealing=true \ main.number_of_macro_cycles=10
Best regards,
Blaine
********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center
Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419
office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
________________________________________ From: [email protected] [[email protected]] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [[email protected]] Sent: Tuesday, November 10, 2009 12:12 PM To: '[email protected]' Subject: [phenixbb] Glycan refinement
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don't know how to do the "apply_cif_link' for the extensions such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated.
Thanks,
Tongqing
Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Engin, I had already gotten as far as the using BMA and MAN. I will give the stereochemistry of my glycans another close examination after reading the papers that you referred to. I think novice refiners of glycoprotein structures like myself grossly underestimate the care required to refine glycan structures correctly. Thank you for pointing out the linkage types. I will give those a try since restraints beyond a simple distance restraint should improve my model. Thank you for your suggestions! Best regards, Blaine ********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877 ________________________________________ From: [email protected] [[email protected]] On Behalf Of Engin Ozkan [[email protected]] Sent: Tuesday, November 10, 2009 1:36 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Glycan refinement Hi Blaine, That might not work correctly. You may get the stereochemistry of the linkage incorrect if you use just a bond distance restraint. You should use linkage types like BETA1-4, or ALPHA1-6, depending on the type of the linkage. And as I have mentioned in the email before, you should also call your beta mannose BMA, and alpha mannose MAN (see the references I mentioned in that email). So something like this would be my guess: apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 902 residue_selection_2 = chain A and resname BMA and resid 903 } apply_cif_link { data_link = ALPHA1-6 residue_selection_1 = chain A and resname BMA and resid 903 residue_selection_2 = chain A and resname MAN and resid 904 } Please correct me if I am wrong. Engin On 11/10/09 11:23 AM, Mooers, Blaine H.M. (HSC) wrote:
Hi Tongqing,
Make a sugars.edits ascii file with links like the following between two manoses
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name O2 and chain A and resname MAN and resseq 1490 atom_selection_2 = name C1 and chain A and resname MAN and resseq 1491 distance_ideal = 1.439000 sigma = 0.020 } }
and then include this file when running phenix.refine in the command mode, e.g.
phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \ refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \ strategy=individual_sites+individual_adp simulated_annealing=true \ main.number_of_macro_cycles=10
Best regards,
Blaine
********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center
Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419
office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
________________________________________ From: [email protected] [[email protected]] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [[email protected]] Sent: Tuesday, November 10, 2009 12:12 PM To: '[email protected]' Subject: [phenixbb] Glycan refinement
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
Thanks,
Tongqing
Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Blaine, You are not alone. We recently discovered a few structures deposited with incorrect geometries and naming by former lab members. It was embarrassing, so we are all paying extra attention now. Getting as much help as possible from refinement and validation software is the smart thing to do. Engin On 11/10/09 11:59 AM, Mooers, Blaine H.M. (HSC) wrote:
Hi Engin,
I had already gotten as far as the using BMA and MAN. I will give the stereochemistry of my glycans another close examination after reading the papers that you referred to. I think novice refiners of glycoprotein structures like myself grossly underestimate the care required to refine glycan structures correctly.
Thank you for pointing out the linkage types. I will give those a try since restraints beyond a simple distance restraint should improve my model.
Thank you for your suggestions!
Best regards,
Blaine
********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center
Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419
office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
________________________________________ From: [email protected] [[email protected]] On Behalf Of Engin Ozkan [[email protected]] Sent: Tuesday, November 10, 2009 1:36 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Glycan refinement
Hi Blaine,
That might not work correctly. You may get the stereochemistry of the linkage incorrect if you use just a bond distance restraint. You should use linkage types like BETA1-4, or ALPHA1-6, depending on the type of the linkage. And as I have mentioned in the email before, you should also call your beta mannose BMA, and alpha mannose MAN (see the references I mentioned in that email).
So something like this would be my guess:
apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 902 residue_selection_2 = chain A and resname BMA and resid 903 } apply_cif_link { data_link = ALPHA1-6 residue_selection_1 = chain A and resname BMA and resid 903 residue_selection_2 = chain A and resname MAN and resid 904 }
Please correct me if I am wrong.
Engin
On 11/10/09 11:23 AM, Mooers, Blaine H.M. (HSC) wrote:
Hi Tongqing,
Make a sugars.edits ascii file with links like the following between two manoses
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name O2 and chain A and resname MAN and resseq 1490 atom_selection_2 = name C1 and chain A and resname MAN and resseq 1491 distance_ideal = 1.439000 sigma = 0.020 } }
and then include this file when running phenix.refine in the command mode, e.g.
phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \ refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \ strategy=individual_sites+individual_adp simulated_annealing=true \ main.number_of_macro_cycles=10
Best regards,
Blaine
********************************************************** Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center
Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419
office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 email: [email protected] http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
________________________________________ From: [email protected] [[email protected]] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [[email protected]] Sent: Tuesday, November 10, 2009 12:12 PM To: '[email protected]' Subject: [phenixbb] Glycan refinement
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
Thanks,
Tongqing
Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
This question just seems to come again and again. Search on the web with phenixbb and glycan or mannose, etc. You'll see the answer. I do have a related question to the developers, however. In recent articles published, it was pointed out that 30% of glycoproteins in the pdb had incorrect geometries and names for sugars (Lutteke, Frank, von der Lieth, Carbohydrate Research, 2004; Crispin, Stuart, Jones, NSMB, 2007). The most common error apparently is the alpha mannose having beta geometry, and vice versa. We are also told that beta mannose should have the three-letter code BMA, and alpha mannose is MAN, which is a nice convention to follow. Unfortunately, this convention is not always followed by users, and monomer libraries come with definitions for both alpha and beta anomers called the same three-letter code. The fact that both stereoisomers are found in the same glycosylation chain in all eukaryotes, actually linked to each other, makes an ugly sight. This is like having a polypeptide chain of L-Ala linked to D-Ala, and calling it Ala-Ala, which would cause confusion. Of course, if the person who modeled the structure knows to use the correct cif link, the stereochemistry is correct, but it will not be clear to people looking at the sequence or even at the actual structure; rules for defining anomers are complicated. (Just to make things worse, I don't currently see a BMA.cif in the phenix monomer library, although it is in the list file. Thankfully, there is a MAN-b-D, which one can modify to have a three-letter code of BMA. Or one can use the ccp4 monomer library for a BMA cif file). Would the developers creating the extremely useful monomer libraries be interested in taking into account naming conventions for glycoproteins to help new users avoid confusion and possibly mistakes? There is now software for checking proteoglycan naming and chemistries (Lutteke, von der Lieth, BMC Bionformatics, 2004; Berman, Henrick, Nakamura, Markley, NSMB, 2007), and it would also be great incorporating these into validation tools that come with PHENIX, if possible. Nucleic acids and polypeptides might be special, but glycosylation deserves some attention, too, and I believe PDB now sends you warnings if you are trying to deposit structures with incorrectly modeled glycans. Thanks, Engin On 11/10/09 10:12 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
Thanks,
Tongqing
*Tongqing Zhou, Ph.D. *
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
*/******************************************************************/*//
*/The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives./*
*/******************************************************************/*
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Hi Engin, It is absolutely true that carbohydrates need much more attention than they got from us. Thanks for all your advice. I hope it helps people make do with the existing facilities until we find the time to implement better solutions. Ralf
participants (5)
-
Engin Ozkan -
junfeng liu -
Mooers, Blaine H.M. (HSC) -
Ralf W. Grosse-Kunstleve -
Zhou, Tongqing (NIH/VRC) [E]