3KD9 | pdb_00003kd9

Crystal structure of pyridine nucleotide disulfide oxidoreductase from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb3KD9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-22 Released: 2009-11-10 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Crystal structure of pyridine nucleotide disulfide oxidoreductase from Pyrococcus horikoshii

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 148.73 kDa 
• Atom Count: 9,568 
• Modeled Residue Count: 1,254 
• Deposited Residue Count: 1,347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme A disulfide reductase	A, B, C	449	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH0572 EC: 1.8.1.14 (PDB Primary Data), 1.8.1 (UniProt)
UniProt
Find proteins for O58308 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58308  Go to UniProtKB:  O58308

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.81	α = 90
b = 114.81	β = 90
c = 353.917	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
Coot	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references