7TMD

Crystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb7TMD/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-19 Released: 2022-02-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.240 
• R-Value Work: 0.171 
• R-Value Observed: 0.175 

Literature

Crystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae

Lovell, S., Liu, L., Battaile, K.P., Tillery, L., Shek, R., Craig, J.K., Barrett, L.K., Van Voorhis, W.C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 225.75 kDa 
• Atom Count: 15,546 
• Modelled Residue Count: 1,978 
• Deposited Residue Count: 2,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C, D, E, F	342	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0  Gene Names: KPHS_05120 EC: 2.1.3.3
UniProt
Find proteins for A0A0H3GHJ1 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GHJ1  Go to UniProtKB:  A0A0H3GHJ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
BR	H [auth A], I [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.240 
• R-Value Work: 0.171 
• R-Value Observed: 0.175 
• Space Group: I 1 2 1
• Diffraction Data: https://doi.org/10.18430/M37TMD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.093	α = 90
b = 154.714	β = 91.04
c = 150.557	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description