2PYA | pdb_00002pya

Ultra-high resolution structure of P. abyssi rubredoxin W4L/R5S/A44S

• PDB DOI: https://doi.org/10.2210/pdb2PYA/pdb

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


• Deposited: 2007-05-16 Released: 2008-04-29 
• Deposition Author(s): Boenisch, H., Ladenstein, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free: 
  0.105 (Depositor) 
• R-Value Work: 
  0.097 (DCC) 
• R-Value Observed: 
  0.098 (Depositor) 

Literature

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O-H...Sgamma-Fe hydrogen bond increased the reduction potential by 65 mV.

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

(2007) J Biol Inorg Chem 12: 1163-1171

• PubMed: 17712580 
• DOI: https://doi.org/10.1007/s00775-007-0289-8
• Primary Citation Related Structures: 
  2PYA


• PubMed Abstract: 
  

  The effect of D-H...S(gamma)-Fe hydrogen bonding on the reduction potential of rubredoxin was investigated by the introduction of an O-H...S(gamma)-Fe hydrogen bond on the surface of Pyrococcus abyssi rubredoxin. The formation of a weak hydrogen bond between Ser44-O(gamma) and Cys42-S(gamma) in mutant W4L/R5S/A44S increased the reduction potential by 56 mV. When side effects of the mutation were taken into account, the contribution of the additional cluster hydrogen bond to the reduction potential was estimated to be +65 mV. The structural analysis was based on ultrahigh-resolution structures of oxidized P. abyssi rubredoxin W4L/R5S and W4L/R5S/A44S refined to 0.69 and 0.86 A, respectively.

---

Organizational Affiliation: 
• Center of Biosciences, Karolinska Institutet, Hälsovägen 7-9, 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: 5.89 kDa 
• Atom Count: 548 
• Modeled 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): 3  Gene Names: rub
UniProt
Find proteins for Q9V099 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V099  Go to UniProtKB:  Q9V099

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free:  0.105 (Depositor) 
• R-Value Work:  0.097 (DCC) 
• R-Value Observed: 0.098 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.385	α = 90
b = 39.812	β = 90
c = 45.117	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELXD	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Boenisch, H., Ladenstein, R.

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection