[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
> 



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