6RXN

THE STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO DESULFURICANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.093 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution.

Stenkamp, R.E.Sieker, L.C.Jensen, L.H.

(1990) Proteins 8: 352-364

  • DOI: 10.1002/prot.340080409
  • Primary Citation of Related Structures:  
    6RXN

  • PubMed Abstract: 
  • The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 A resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0 ...

    The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 A resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 A resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.


    Related Citations: 
    • Structure of Rubredoxin from the Bacterium Desulfovibrio Desulfuricans
      Sieker, L.C., Stenkamp, R.E., Jensen, L.H., Prickril, B., Legall, J.
      (1986) FEBS Lett 208: 73
    • Crystallographic Study of Rubredoxin from the Bacterium Desulfovibrio Desulfuricans Strain 27774
      Sieker, L.C., Jensen, L.H., Pickril, B.C., Legall, J.
      (1983) J Mol Biol 171: 101

    Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle 98195.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RUBREDOXINA46Desulfovibrio desulfuricansMutation(s): 0 
UniProt
Find proteins for P04170 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore P04170 
Go to UniProtKB:  P04170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04170
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.093 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.92α = 101
b = 17.79β = 83.4
c = 19.72γ = 104.5
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1991-01-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other