5OME

The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)

• PDB DOI: https://doi.org/10.2210/pdb5OME/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-07-31 Released: 2018-09-05 
• Deposition Author(s): Cuypers, M.G., Mason, S.A., Mossou, E., Haertlein, M., Mitchell, E.P., Forsyth, V.T.
• Funding Organization(s): Engineering and Physical Sciences Research Council, European Union, ESRF, Institut Laue-Langevin

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free: 
  0.121 (Depositor), 0.120 (DCC) 
• R-Value Work: 
  0.111 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.112 (Depositor) 

Literature

The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)

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

To be published.

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: 6.3 kDa 
• Atom Count: 706 
• Modelled 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
PO4	D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free:  0.121 (Depositor), 0.120 (DCC) 
• R-Value Work:  0.111 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.993	α = 90
b = 34.803	β = 90
c = 43.233	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Cuypers, M.G., Mason, S.A., Mossou, E., Haertlein, M., Mitchell, E.P., Forsyth, V.T.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/C015452/1
European Union	France	RII3-CT-2003-505925
ESRF	France	--
Institut Laue-Langevin	France	--

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2023-02-15
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2023-02-22
  Changes: Advisory
• Version 1.3: 2024-06-19
  Changes: Data collection