Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a.

Vitali, J.Carroll, D.Chaudhry, R.G.Hackert, M.L.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1978-1985

  • DOI: https://doi.org/10.1107/s0907444999010756
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ornithine decarboxylases catalyze the conversion of ornithine to putrescine at the beginning of the polyamine pathway. Ornithine decarboxylase (ODC) from Lactobacillus 30a is a 990612 Da dodecamer composed of six homodimers. A single point mutation (Gly121Tyr) was found to prevent association of dimers into dodecamers. The dimeric protein has been crystallized at pH 7.0 in the presence of guanosine triphosphate (GTP). Crystals belong to space group P3(2)21, with unit-cell parameters a = 111.8, c = 135.9 A and one monomer in the asymmetric unit. The structure was determined by molecular replacement and refined using simulated annealing to R = 0.211 at 2. 7 A resolution. The GTP-binding site was analyzed in detail. The protein exhibits a novel binding mode for GTP which is different from that seen in most G-proteins or GTPases. Central to this binding scheme appear to be three lysines, Lys190, Lys374 and Lys382, which form salt bridges with the three phosphates, and Thr191, which hydrogen bonds with the guanine base. Furthermore, the structure suggests that there is some flexibility in the wing domain, which can change its orientation as the protein adapts to its environment. The active site is similar to that of the native enzyme, consistent with the observation that the enzyme activity does not depend on its dodecameric state.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (ORNITHINE DECARBOXYLASE)730Lactobacillus sp. 30AMutation(s): 1 
Find proteins for P43099 (Lactobacillus sp. (strain 30a))
Explore P43099 
Go to UniProtKB:  P43099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43099
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GTP

Download Ideal Coordinates CCD File 
C10 H16 N5 O14 P3
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.8α = 90
b = 111.8β = 90
c = 135.9γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.6: 2023-08-09
    Changes: Data collection, Refinement description