2WT9 | pdb_00002wt9

Acinetobacter baumanii nicotinamidase pyrazinamidease

PDB DOI: https://doi.org/10.2210/pdb2WT9/pdb

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

Deposited: 2009-09-15 Released: 2009-11-10
Deposition Author(s): Fyfe, P.K., Rao, V.A., Zemla, A., Cameron, S., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.235 (Depositor), 0.248 (DCC)
R-Value Work:
0.179 (Depositor), 0.193 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Specificity and Mechanism of Acinetobacter Baumanii Nicotinamidase: Implications for Activation of the Front-Line Tuberculosis Drug Pyrazinamide.

Fyfe, P.K., Rao, V.A., Zemla, A., Cameron, S., Hunter, W.N.

(2009) Angew Chem Int Ed Engl 48: 9176

PubMed: 19859929 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.200903407
Primary Citation Related Structures:
2WT9, 2WTA

Organizational Affiliation

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Macromolecule Content

Total Structure Weight: 52.84 kDa
Atom Count: 3,709
Modeled Residue Count: 415
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NICOTINAMIDASE	A, B	235	Acinetobacter baumannii AYE	Mutation(s): 0 EC: 3.5.1.19

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NIO Query on NIO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	NICOTINIC ACID C₆ H₅ N O₂ PVNIIMVLHYAWGP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.235 (Depositor), 0.248 (DCC)
R-Value Work: 0.179 (Depositor), 0.193 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.64	α = 113.19
b = 46.89	β = 88.25
c = 59.48	γ = 115.61

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-11-09
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Version format compliance
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description