1YK4

Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S

• PDB DOI: https://doi.org/10.2210/pdb1YK4/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-01-17 Released: 2006-01-17 
• Deposition Author(s): Bonisch, H., Schmidt, C.L., Bianco, P., Ladenstein, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.69 Å
• R-Value Free: 0.108 
• R-Value Work: 0.100 
• R-Value Observed: 0.100 

Literature

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.

Bonisch, H., Schmidt, C.L., Bianco, P., Ladenstein, R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 990-1004

• PubMed: 15983423 
• DOI: https://doi.org/10.1107/S090744490501293X
• Primary Citation of Related Structures:  
  1YK4, 1YK5


• PubMed Abstract: 
  

  The crystal structure of Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved by direct methods. The model of the air-oxidized protein was refined by partially restrained full-matrix least-squares refinement against intensity data to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin provides very detailed and precise information about the Fe(SCys)(4) centre and its environment, the peptide-backbone stereochemistry, H atoms and hydrogen bonds, static and dynamic disorder, the solvent structure and the electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a series of mutants studied by atomic and ultrahigh-resolution X-ray crystallography which are expected to contribute to the understanding of structure-function relationships in iron-sulfur proteins.

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Organizational Affiliation: 

Karolinska Institutet, Department of Biosciences at NOVUM, Center for Structural Biochemistry, Hälsovägen 7-9, S-14157 Huddinge, Sweden. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.83 kDa 
• Atom Count: 566 
• Modelled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	52	Pyrococcus abyssi	Mutation(s): 2  Gene Names: rub
UniProt
Find proteins for Q9V099 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V099  Go to UniProtKB:  Q9V099

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: 0.69 Å
• R-Value Free: 0.108 
• R-Value Work: 0.100 
• R-Value Observed: 0.100 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.14	α = 90
b = 39.5	β = 90
c = 45.07	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): Bonisch, H., Schmidt, C.L., Bianco, P., Ladenstein, R.

Revision History  

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection