Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43478.79 
• Atom Count: 2834 
• Residue Count: 382 
• Unique protein chains: 1

3ZPG

Acinetobacter baumannii RibD, form 2

• DOI: 10.2210/pdb3ZPG/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)
• Expression System: Escherichia coli BL21(DE3)


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.237 
• R-Value Work: 0.214 

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 69: 611

• PubMed: 23722836 
• DOI: 10.1107/S174430911301292X
• Primary Citation of Related Structures:  
  3ZPC


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RIBD	A	382	Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)	Mutation(s): 0  Gene Names: ribD
Find proteins for D0CB74 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Go to UniProtKB:  D0CB74

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXL	A	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
5GP	A	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
CAC	A	CACODYLATE ION dimethylarsinate C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.237 
• R-Value Work: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 72.998	α = 90.00
b = 72.998	β = 90.00
c = 201.456	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2013-03-27
  Type: Initial release
• Version 1.1: 2013-06-12
  Type: Database references
• Version 1.2: 2017-06-28
  Type: Data collection