2DM9

Crystal Structure of PH1978 from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2DM9/pdb

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


• Deposited: 2006-04-20 Released: 2007-01-16 
• Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.259 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal Structure of PH1978 from Pyrococcus horikoshii OT3

Lokanath, N.K., 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)

Macromolecule Content

• Total Structure Weight: 45.85 kDa 
• Atom Count: 2,041 
• Modelled Residue Count: 236 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit E	A, B	198	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: atpE EC: 3.6.3.14
UniProt
Find proteins for O57724 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57724  Go to UniProtKB:  O57724

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.259 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.196	α = 90
b = 55.317	β = 90
c = 77.481	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-16
  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