2D0I | pdb_00002d0i

Crystal Structure PH0520 protein from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2D0I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-02 Released: 2006-02-02 
• Deposition Author(s): Lokanath, N.K., Terao, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Crystal Structure PH0520 protein from Pyrococcus horikoshii OT3

Lokanath, N.K., Terao, Y., Kunishima, N.

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: 152.45 kDa 
• Atom Count: 11,762 
• Modeled Residue Count: 1,332 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dehydrogenase	A, B, C, D	333	Pyrococcus horikoshii OT3	Mutation(s): 0
UniProt
Find proteins for O58256 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58256  Go to UniProtKB:  O58256

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.756	α = 90
b = 63.739	β = 103.14
c = 131.978	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-02 
Deposition Author(s): Lokanath, N.K., Terao, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-02-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references