1RYT

RUBRERYTHRIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains.

deMare, F., Kurtz Jr., D.M., Nordlund, P.

(1996) Nat Struct Biol 3: 539-546

  • DOI: 10.1038/nsb0696-539
  • Primary Citation of Related Structures:  
    1RYT

  • PubMed Abstract: 

    • We have determined the structure of rubrerythrin, a non-haem iron protein from the anaerobic sulphate-reducing bacterium, Desulfovibrio vulgaris (Hildenborough), by X-ray crystallography. The structure reveals a tetramer of two-domain subunits. Each subu ...

    We have determined the structure of rubrerythrin, a non-haem iron protein from the anaerobic sulphate-reducing bacterium, Desulfovibrio vulgaris (Hildenborough), by X-ray crystallography. The structure reveals a tetramer of two-domain subunits. Each subunit contains a four-helix bundle surrounding a diiron-oxo site and a C-terminal rubredoxin-like FeS4 domain. The diiron-oxo site contains a larger number of carboxylate ligands and a higher degree of solvent exposure than do those in other diiron-oxo proteins. The four-helix bundle of rubrerythrin closely resembles those of the ferritin and bacterioferritin subunits, suggesting a relationship among these proteins-consistent with the recently demonstrated ferroxidase activity of rubrerythrin.

    Organizational Affiliation: 

    Department of Molecular Biology, Stockholm University, Sweden.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RUBRERYTHRIN A190Desulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: rbr, DVU_3094
Find proteins for P24931 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Explore P24931 
Go to UniProtKB:  P24931
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE
Download Ideal Coordinates CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.4α = 90
b = 82β = 90
c = 100.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance