2DMA | pdb_00002dma

Crystal Structure of PH1978 from Pyrococcus horikoshii OT3 (form II)

• PDB DOI: https://doi.org/10.2210/pdb2DMA/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.05 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PH1978 from Pyrococcus horikoshii OT3 (form II)

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 23.16 kDa 
• Atom Count: 1,014 
• Modeled Residue Count: 118 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit E	A	198	Pyrococcus horikoshii OT3	Mutation(s): 5  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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.235	α = 90
b = 78.067	β = 90
c = 52.829	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	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: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-16
  Changes: Structure summary