4WBF | pdb_00004wbf

Acinetobacter baumannii SDF NDK

PDB DOI: https://doi.org/10.2210/pdb4WBF/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii SDF
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-09-03 Released: 2015-06-17
Deposition Author(s): Hu, Y., Liu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.258 (Depositor), 0.263 (DCC)
R-Value Work:
0.201 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structural and Functional Characterization of Acinetobacter baumannii Nucleoside Diphosphate Kinase

Hu, Y., Feng, F., Liu, Y.

(2015) PROG BIOCHEM BIOPHYS 42: 260-267

DOI: https://doi.org/10.16476/j.pibb.2014.0319

Macromolecule Content

Total Structure Weight: 15.34 kDa
Atom Count: 1,100
Modeled Residue Count: 140
Deposited Residue Count: 142
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A	142	Acinetobacter baumannii SDF	Mutation(s): 0 Gene Names: ndk, ABSDF3006 EC: 2.7.4.6
UniProt
Find proteins for B0VKS3 (Acinetobacter baumannii (strain SDF)) Explore B0VKS3 Go to UniProtKB: B0VKS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0VKS3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.258 (Depositor), 0.263 (DCC)
R-Value Work: 0.201 (Depositor), 0.205 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.33	α = 90
b = 75.4	β = 90
c = 82.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-17
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy

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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.