3HDJ | pdb_00003hdj

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

• PDB DOI: https://doi.org/10.2210/pdb3HDJ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bordetella pertussis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-07 Released: 2009-05-19 
• Deposition Author(s): Tan, K., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.212 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

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

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.23 kDa 
• Atom Count: 5,259 
• Modeled Residue Count: 622 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ornithine cyclodeaminase	A, B	313	Bordetella pertussis	Mutation(s): 0  Gene Names: Bordetella pertussis, BP0354
UniProt
Find proteins for Q7VSP8 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VSP8  Go to UniProtKB:  Q7VSP8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	I [auth A], M [auth B], N [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.212 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.405	α = 90
b = 50.923	β = 100.98
c = 106.999	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Tan, K., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary