[phenixbb] distorted (collapsed) zinc-finger motifs

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Tue Dec 7 11:58:26 PST 2010


Hi Hasan,

The pdb file you sent (zinc_finger.pdb) has heavily distorted geometry
around the zinc finger, with the SG forming disulfide bonds and the ZN
pushed far away from the center of the four SG. I suggest you discard
that pdb file and go back to an earlier version where the geometry is
still intact. Then phenix.refine should work automatically with the
zn_link and apply_cif_link files as is. You can remove the
disulfide_distance_cutoff re-assignment at the top of your apply_cif_link
file.
(I just tried 3a9j from the pdb and it works without a problem.)

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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