3GD5

Crystal structure of ornithine carbamoyltransferase from Gloeobacter violaceus

• PDB DOI: https://doi.org/10.2210/pdb3GD5/pdb

• Classification: TRANSFERASE
• Organism(s): Gloeobacter violaceus PCC 7421
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-23 Released: 2009-04-14 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Ramagopal, U.A., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.271 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 

Literature

Crystal structure of ornithine carbamoyltransferase from Gloeobacter violaceus

Fedorov, A.A., Fedorov, E.V., Toro, R., Ramagopal, U.A., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 211.28 kDa 
• Atom Count: 13,303 
• Modelled Residue Count: 1,710 
• Deposited Residue Count: 1,938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C, D, E, F	323	Gloeobacter violaceus PCC 7421	Mutation(s): 0  Gene Names: argF, gll3101 EC: 2.1.3.3
UniProt
Find proteins for Q7NGR7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NGR7  Go to UniProtKB:  Q7NGR7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.271 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.563	α = 90
b = 142.423	β = 90
c = 149.273	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
Auto-Rickshaw	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Ramagopal, U.A., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references