1VDZ | pdb_00001vdz

Crystal structure of A-type ATPase catalytic subunit A from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1VDZ/pdb

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


• Deposited: 2004-03-26 Released: 2005-06-21 
• Deposition Author(s): Maegawa, Y., Morita, H., Yao, M., Watanabe, N., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Crystal structure of A-type ATPase catalytic subunit A from Pyrococcus horikoshii OT3

Maegawa, Y., Morita, H., Yao, M., Watanabe, N., Tanaka, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.79 kDa 
• Atom Count: 4,033 
• Modeled Residue Count: 513 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A-type ATPase subunit A	A	588	Pyrococcus horikoshii	Mutation(s): 0  EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for O57728 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57728  Go to UniProtKB:  O57728

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.977	α = 90
b = 127.977	β = 90
c = 104.732	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-21 
Deposition Author(s): Maegawa, Y., Morita, H., Yao, M., Watanabe, N., Tanaka, I.

Revision History  

• Version 1.0: 2005-06-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations