3ZPG | pdb_00003zpg

Acinetobacter baumannii RibD, form 2

PDB DOI: https://doi.org/10.2210/pdb3ZPG/pdb

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

Deposited: 2013-02-27 Released: 2013-03-27
Deposition Author(s): Dawson, A., Trumper, P., Chrysostomou, G., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.237 (Depositor), 0.231 (DCC)
R-Value Work:
0.214 (Depositor), 0.212 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of Diaminohydroxyphosphoribosylaminopyrimidine Deaminase/5-Amino-6-(5-Phosphoribosylamino)Uracil Reductase from Acinetobacter Baumannii.

Dawson, A., Trumper, P., Chrysostomou, G., Hunter, W.N.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 611

PubMed: 23722836 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S174430911301292X
Primary Citation Related Structures:
3ZPC, 3ZPG

PubMed Abstract:
The bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase (RibD) represents a potential antibacterial drug target. The structure of recombinant Acinetobacter baumannii RibD is reported in orthorhombic and tetragonal crystal forms at 2.2 and 2.0 Å resolution, respectively. Comparisons with orthologous structures in the Protein Data Bank indicated close similarities. The tetragonal crystal form was obtained in the presence of guanosine monophosphate, which surprisingly was observed to occupy the adenine-binding site of the reductase domain.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 43.48 kDa
Atom Count: 2,961
Modeled Residue Count: 354
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBD	A	382	Acinetobacter baumannii	Mutation(s): 0 EC: 3.5.4.26 (PDB Primary Data), 1.1.1.193 (PDB Primary Data)
UniProt
Find proteins for D0CB74 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CB74 Go to UniProtKB: D0CB74
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0CB74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP Query on 5GP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth A] mmCIF format, chain E [auth A]	E [auth A], K [auth A]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain K [auth A]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
OXL Query on OXL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [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]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.237 (Depositor), 0.231 (DCC)
R-Value Work: 0.214 (Depositor), 0.212 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.998	α = 90
b = 72.998	β = 90
c = 201.456	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2013-06-12
Changes: Database references
Version 1.2: 2017-06-28
Changes: Data collection
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description