6RXN | pdb_00006rxn

THE STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO DESULFURICANS

• PDB DOI: https://doi.org/10.2210/pdb6RXN/pdb

• Classification: ELECTRON TRANSFER(IRON-SULFUR PROTEIN)
• Organism(s): Desulfovibrio desulfuricans
• Mutation(s): No 


• Deposited: 1990-01-16 Released: 1991-01-15 
• Deposition Author(s): Stenkamp, R.E., Sieker, L.C., Jensen, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 
  0.095 (DCC) 
• R-Value Observed: 
  0.093 (Depositor) 

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

• PubMed: 2091025 
• DOI: https://doi.org/10.1002/prot.340080409
• Primary Citation 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 0.093 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.

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Organizational Affiliation: 
• Department of Biological Structure, University of Washington, Seattle 98195.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.19 kDa 
• Atom Count: 491 
• Modeled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUBREDOXIN	A	46	Desulfovibrio desulfuricans	Mutation(s): 0
UniProt
Find proteins for P04170 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore P04170  Go to UniProtKB:  P04170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work:  0.095 (DCC) 
• R-Value Observed: 0.093 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.92	α = 101
b = 17.79	β = 83.4
c = 19.72	γ = 104.5

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-01-15 
Deposition Author(s): Stenkamp, R.E., Sieker, L.C., Jensen, L.H.

Revision History  

• 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
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary