4S0M | pdb_00004s0m

Crystal Structure of nucleoside diphosphate kinase at 1.92 A resolution from acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb4S0M/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-01-02 Released: 2015-02-11
Deposition Author(s): Sikarwar, J., Shukla, P.K., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.259 (Depositor), 0.256 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.213 (Depositor)

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

Literature

Crystal Structure of nucleoside diphosphate kinase at 1.92 A resolution from Acinetobacter baumannii

Sikarwar, J., Shukla, P.K., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 123.92 kDa
Atom Count: 9,552
Modeled Residue Count: 1,144
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A B C D E [auth F] A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I]	143	Acinetobacter baumannii	Mutation(s): 0 Gene Names: ABBL099_02780, BL01_17035, FL75_03050, FL80_07750, GQ86_04945, IOMTU433_3298, IX87_17090, LX00_02580, ndk, P795_14800 EC: 2.7.4.6
UniProt
Find proteins for V5VIC4 (Acinetobacter baumannii) Explore V5VIC4 Go to UniProtKB: V5VIC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5VIC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth G] SDF format, chain I [auth D] MOL2 format, chain J [auth G] MOL2 format, chain I [auth D] mmCIF format, chain J [auth G] mmCIF format, chain I [auth D]	I [auth D], J [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain J [auth G] Interactions & Density Focus chain I [auth D] Focus chain J [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.259 (Depositor), 0.256 (DCC)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.924	α = 90
b = 71.381	β = 93.71
c = 129.427	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, 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.