2CWK | pdb_00002cwk

Crystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb2CWK/pdb

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

Deposited: 2005-06-21 Released: 2005-12-21
Deposition Author(s): Kato-Murayama, M., Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.209 (Depositor), 0.208 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2CWK

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

Literature

Crystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii

Kato-Murayama, M., Murayama, K., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.68 kDa
Atom Count: 2,800
Modeled Residue Count: 305
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nucleoside-diphosphate kinase	A, B	160	Pyrococcus horikoshii OT3	Mutation(s): 0 EC: 2.7.4.6
UniProt
Find proteins for O58429 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58429 Go to UniProtKB: O58429
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58429
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.209 (Depositor), 0.208 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.065	α = 90
b = 116.065	β = 90
c = 192.833	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-12-21

Deposition Author(s):

Kato-Murayama, M.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-12-21
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

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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.