2EF0 | pdb_00002ef0

Crystal structure of ornithine carbamoyltransferase from thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2EF0/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-19 Released: 2007-04-13 
• Deposition Author(s): Karthe, P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ornithine carbamoyltransferase from thermus thermophilus

Karthe, P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.33 kDa 
• Atom Count: 2,387 
• Modeled Residue Count: 287 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A	301	Thermus thermophilus HB8	Mutation(s): 0  EC: 2.1.3.3
UniProt
Find proteins for Q5SJ15 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ15  Go to UniProtKB:  Q5SJ15

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.385	α = 90
b = 77.385	β = 90
c = 79.132	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-13 
Deposition Author(s): Karthe, P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description