[phenixbb] distorted (collapsed) zinc-finger motifs
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Mon Dec 6 17:56:39 PST 2010
Hi Hasan,
Did you look at the .geo file already to check if the bond and angle restraints
are correct for the atoms involved?
The .geo file can be very large if you have a large model. An option to reduce
the noise for troubleshooting is to cut down the pdb file to just the residues
involved
and then run phenix.refine --dry-run with the small pdb file. If you get stuck,
we could help more if you send us the small pdb file.
Ralf
----- Original Message ----
> From: Hasan Demirci <demircha99 at gmail.com>
> To: phenixbb at phenix-online.org
> Sent: Mon, December 6, 2010 5:47:28 PM
> Subject: [phenixbb] distorted (collapsed) zinc-finger motifs
>
> Hi,
>
> I am in the middle of refining a 3.5 A (low resolution)
> ribonucleo-protein complex structure.
> Two of the proteins in this complex contain "zinc-finger" motif.
> These zinc-finger motifs instead of forming a cysteine-zinc
> interactions, cysteines are forming di or in these case tetra-sulfide
> bridges.
> Initially, zinc is centered but after refinement 4 cysteines come out
> collapsed and forming covalent bonds to each other and also distorted
> and zinc is not at the center anymore.
>
>
> Below is the phenix.refine zn_link.param file I am using.
>
> Many thanks for advice,
> Hasan Demirci
> ----------------------------------------------------------------------------
>
>
> refinement.pdb_interpretation {
> disulfide_distance_cutoff = 0.1
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain D and resname ZN and resid 306
> residue_selection_2 = chain D and resname CYS and resid 9
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain D and resname ZN and resid 306
> residue_selection_2 = chain D and resname CYS and resid 12
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain D and resname ZN and resid 306
> residue_selection_2 = chain D and resname CYS and resid 26
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain D and resname ZN and resid 306
> residue_selection_2 = chain D and resname CYS and resid 31
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain N and resname ZN and resid 307
> residue_selection_2 = chain N and resname CYS and resid 24
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain N and resname ZN and resid 307
> residue_selection_2 = chain N and resname CYS and resid 27
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain N and resname ZN and resid 307
> residue_selection_2 = chain N and resname CYS and resid 40
> }
> refinement.pdb_interpretation.apply_cif_link {
> data_link = ZN-CYS
> residue_selection_1 = chain N and resname ZN and resid 307
> residue_selection_2 = chain N and resname CYS and resid 43
> }
> #
> data_link_ZN-CYS
> #
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
> ZN-CYS 1 ZN 2 SG single 2.340 0.020
> loop_
> _chem_link_angle.link_id
> _chem_link_angle.atom_1_comp_id
> _chem_link_angle.atom_id_1
> _chem_link_angle.atom_2_comp_id
> _chem_link_angle.atom_id_2
> _chem_link_angle.atom_3_comp_id
> _chem_link_angle.atom_id_3
> _chem_link_angle.value_angle
> _chem_link_angle.value_angle_esd
> ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000
>
>----------------------------------------------------------------------------------------------------
>-
>
>
>
> --
> Hasan DeMirci, Ph.D.
> Postdoctoral Fellow
> Department of Molecular Biology, Cellular Biology & Biochemistry
> Brown University
> 185 Meeting Street
> Providence, RI 02912
>
> (401) 863-3652 lab (SFH)
> (401) 863-6124 lab (ship st)
> (401) 226-7852 cell
>
> Hasan_DeMirci at Brown.edu
> demircha99 at gmail.com
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
More information about the phenixbb
mailing list