5X00 | pdb_00005x00

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 (Depositor), 0.261 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 236
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.261 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

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

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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

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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.