1RYT | pdb_00001ryt

RUBRERYTHRIN

• PDB DOI: https://doi.org/10.2210/pdb1RYT/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): No 


• Deposited: 1996-04-26 Released: 1997-05-15 
• Deposition Author(s): Demare, F., Kurtz, D.M., Nordlund, P.

---

Experimental Data Snapshot

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

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

• PubMed: 8646540 
• DOI: https://doi.org/10.1038/nsb0696-539
• Primary Citation 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 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 21.61 kDa 
• Atom Count: 1,568 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUBRERYTHRIN	A	190	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0
UniProt
Find proteins for P24931 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P24931  Go to UniProtKB:  P24931

Small Molecules

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

Experimental Data & Validation

Experimental Data

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

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.4	α = 90
b = 82	β = 90
c = 100.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MARXDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-05-15 
Deposition Author(s): Demare, F., Kurtz, D.M., Nordlund, P.

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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other