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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.271 (Depositor), 0.282 (DCC)
R-Value Work:
0.239 (Depositor), 0.250 (DCC)
R-Value Observed:
0.242 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O57728
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.271 (Depositor), 0.282 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-06-21

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.