4AR3 | pdb_00004ar3

Near-atomic resolution neutron crystallography on the oxidised form perdeuterated Pyrococcus furiosus rubredoxin.

• PDB DOI: https://doi.org/10.2210/pdb4AR3/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-20 Released: 2013-01-16 
• 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: NEUTRON DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.237 (Depositor) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus Furiosus Rubredoxin: Implication of Hydronium Ions and Protonation State Equilibria 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 of 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: 6.18 kDa 
• Atom Count: 613 
• 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 DSM 3638	Mutation(s): 0  Gene Names: rub, PF1282
UniProt
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P24297  Go to UniProtKB:  P24297

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
D3O	G [auth A], H [auth A], I [auth A], J [auth A]	trideuteriooxidanium D3 O XLYOFNOQVPJJNP-ZRLBSURWSA-O
D8U	C [auth A], D [auth A], E [auth A], F [auth A]	deuterium(1+) D GPRLSGONYQIRFK-DYCDLGHISA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.237 (Depositor) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.36	α = 90
b = 35.316	β = 90
c = 43.993	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
RETREAT	data reduction
RETREAT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
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: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Database references
• Version 1.2: 2013-08-14
  Changes: Atomic model
• Version 1.3: 2017-03-22
  Changes: Data collection
• Version 1.4: 2019-08-28
  Changes: Data collection
• Version 2.0: 2021-06-09
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references