5X00

Nucleoside Diphosphate Kinase from Vibrio cholerae is a Thermolabile Type II tetramer

PDB DOI: https://doi.org/10.2210/pdb5X00/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae M66-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-19 Released: 2018-01-31
Deposition Author(s): Agnihotri, P., Mishra, A.K., Pratap, J.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free: 0.258
R-Value Work: 0.228
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Nucleoside Diphosphate Kinase from Vibrio cholerae is a Thermolabile Type II tetramer.

Agnihotri, P., Mishra, A.K., Pratap, J.V.

To be published.

Macromolecule Content

Total Structure Weight: 32.18 kDa
Atom Count: 1,793
Modelled Residue Count: 236
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B	144	Vibrio cholerae M66-2	Mutation(s): 0 Gene Names: ndk, VCM66_0714 EC: 2.7.4.6
UniProt
Find proteins for C3LT09 (Vibrio cholerae serotype O1 (strain M66-2)) Explore C3LT09 Go to UniProtKB: C3LT09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3LT09
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free: 0.258
R-Value Work: 0.228
R-Value Observed: 0.230
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.37	α = 90
b = 71.21	β = 90
c = 89.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-01-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-01-31
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.