5NW3 | pdb_00005nw3

The cryofrozen atomic resolution X-ray crystal structure of perdeuterated Pyrococcus furiosus Rubredoxin (100K, 0.59A resolution)

• PDB DOI: https://doi.org/10.2210/pdb5NW3/pdb

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


• Deposited: 2017-05-04 Released: 2017-06-07 
• Deposition Author(s): Cuypers, M.G., Mason, S.A., Mossou, E., Haertlein, M., Forsyth, V.T.
• Funding Organization(s): Engineering and Physical Sciences Research Council, ILL

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.59 Å
• R-Value Free: 
  0.146 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

The cryofrozen atomic resolution X-ray crystal structure of perdeuterated Pyrococcus furiosus Rubredoxin (100K, 0.59A resolution)

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.24 kDa 
• Atom Count: 658 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.59 Å
• R-Value Free:  0.146 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.622	α = 90
b = 34.533	β = 90
c = 43.071	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: 2017-06-07 
Deposition Author(s): Cuypers, M.G., Mason, S.A., Mossou, E., Haertlein, M., Forsyth, V.T.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--
ILL	France	--

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2024-05-08
  Changes: Advisory, Data collection, Database references, Derived calculations