[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
> _______________________________________________
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>
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