5YOL | pdb_00005yol

Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution

PDB DOI: https://doi.org/10.2210/pdb5YOL/pdb

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

Deposited: 2017-10-29 Released: 2017-11-08
Deposition Author(s): Singh, P.K., Sikarwar, J., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.213 (Depositor), 0.220 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 124.16 kDa
Atom Count: 9,216
Modeled Residue Count: 1,144
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C, D, E A, B, C, D, E, F, G, H	143	Acinetobacter baumannii	Mutation(s): 0 Gene Names: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770... ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330 EC: 2.7.4.6
UniProt
Find proteins for V5VIC4 (Acinetobacter baumannii) Explore V5VIC4 Go to UniProtKB: V5VIC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 T [auth H] SDF format, chain S [auth H] SDF format, chain R [auth G] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain T [auth H] MOL2 format, chain S [auth H] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain T [auth H] mmCIF format, chain S [auth H] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth C] M [auth D] I [auth A], J [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth E], P [auth F], Q [auth G], R [auth G], S [auth H], T [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.213 (Depositor), 0.220 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.1	α = 80.51
b = 69.93	β = 69.94
c = 71.7	γ = 89.76

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-11-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description