4AR5 | pdb_00004ar5

X-ray crystallographic structure of the oxidised form perdeuterated Pyrococcus furiosus rubredoxin in D2O at 295K (in quartz capillary) to 1.00 Angstrom resolution.

• PDB DOI: https://doi.org/10.2210/pdb4AR5/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-20 Released: 2012-12-19 
• Deposition Author(s): Cuypers, M.G., Mason, S.A., Blakeley, M.P., Mitchell, E.P., Haertlein, M., Forsyth, V.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.119 (Depositor), 0.119 (DCC) 
• R-Value Work: 
  0.110 (Depositor), 0.108 (DCC) 
• R-Value Observed: 
  0.110 (Depositor) 

Starting Model: experimental

Literature

Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus Furiosus Rubredoxin: Implication of Hydronium Ions and Protonation Equilibria and Hydronium Ions in Redox Changes

Cuypers, M.G., Mason, S.A., Blakeley, M.P., Mitchell, E.P., Haertlein, M., Forsyth, V.T.

(2013) Angew Chem Int Ed Engl 52: 1022

• PubMed: 23225503 
• DOI: https://doi.org/10.1002/anie.201207071
• Primary Citation Related Structures: 
  4AR3, 4AR4, 4AR5, 4AR6

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Organizational Affiliation: 
• EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 6.09 kDa 
• Atom Count: 608 
• Modeled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUBREDOXIN	A	54	Pyrococcus furiosus	Mutation(s): 0
UniProt
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P24297  Go to UniProtKB:  P24297

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: 1.00 Å
• R-Value Free:  0.119 (Depositor), 0.119 (DCC) 
• R-Value Work:  0.110 (Depositor), 0.108 (DCC) 
• R-Value Observed: 0.110 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.361	α = 90
b = 35.316	β = 90
c = 43.993	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Cuypers, M.G., Mason, S.A., Blakeley, M.P., Mitchell, E.P., Haertlein, M., Forsyth, V.T.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Data collection, Database references
• Version 2.0: 2024-05-01
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description