3F6S

Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin alternate conformers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin.

Guelker, M.Stagg, L.Wittung-Stafshede, P.Shamoo, Y.

(2009) Acta Crystallogr D Biol Crystallogr 65: 523-534

  • DOI: 10.1107/S0907444909010075
  • Primary Citation of Related Structures:  
    3F6S, 3F6R

  • PubMed Abstract: 
  • The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8) ...

    The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3(1)21 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P4(3), which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3(1)21 crystal form. During the early stages of refinement, application of the appropriate twin law, (-h, -k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FlavodoxinA, B, C [auth D], D [auth E], E [auth F], H [auth G], F [auth H], G [auth I]148Desulfovibrio desulfuricansMutation(s): 1 
Gene Names: flavodoxin
UniProt
Find proteins for P26492 (Desulfovibrio desulfuricans)
Explore P26492 
Go to UniProtKB:  P26492
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.226 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.89α = 90
b = 94.89β = 90
c = 238.1γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CNSrefinement
JBluIce-EPICSdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection