2WTA | pdb_00002wta

Acinetobacter baumanii nicotinamidase pyrazinamidease

PDB DOI: https://doi.org/10.2210/pdb2WTA/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: 1.70 Å
R-Value Free:
0.177 (Depositor), 0.201 (DCC)
R-Value Work:
0.147 (Depositor), 0.172 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 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: 26.57 kDa
Atom Count: 1,996
Modeled Residue Count: 213
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VGL Query on VGL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PYRAZINE-2-CARBOXYLIC ACID C₅ H₄ N₂ O₂ NIPZZXUFJPQHNH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF Query on CAF	A	L-PEPTIDE LINKING	C₅ H₁₂ As N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.177 (Depositor), 0.201 (DCC)
R-Value Work: 0.147 (Depositor), 0.172 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.688	α = 90
b = 46.507	β = 101.97
c = 107.602	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2011-11-09
Changes: Database references, Non-polymer description
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary