3ZPG

Acinetobacter baumannii RibD, form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 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

  • DOI: 10.1107/S174430911301292X
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBDA382Acinetobacter baumanniiMutation(s): 0 
EC: 3.5.4.26 (PDB Primary Data), 1.1.1.193 (PDB Primary Data)
Find proteins for D0CB74 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0CB74 
Go to UniProtKB:  D0CB74
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
E [auth A], K [auth A]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
CAC
Query on CAC

Download Ideal Coordinates CCD File 
H [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OXL
Query on OXL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.998α = 90
b = 72.998β = 90
c = 201.456γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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