3HDJ

The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I

Tan, K.Sather, A.Clancy, S.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable ornithine cyclodeaminase
A, B
313Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)Mutation(s): 0 
Find proteins for Q7VSP8 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Go to UniProtKB:  Q7VSP8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.405α = 90.00
b = 50.923β = 100.98
c = 106.999γ = 90.00
Software Package:
Software NamePurpose
WARPmodel building
DMmodel building
HKL-3000data scaling
ARPmodel building
REFMACrefinement
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
DMphasing
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance