3UPD | pdb_00003upd

2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus

• PDB DOI: https://doi.org/10.2210/pdb3UPD/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-17 Released: 2011-12-07 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Winsor, J., Dubrovska, I., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.158 (Depositor) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus.

Minasov, G., Halavaty, A., Shuvalova, L., Winsor, J., Dubrovska, I., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 39.64 kDa 
• Atom Count: 2,745 
• Modeled Residue Count: 346 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A	358	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: argF, VV1_1466 EC: 2.1.3.3
UniProt
Find proteins for Q8DCF5 (Vibrio vulnificus (strain CMCP6)) Explore Q8DCF5  Go to UniProtKB:  Q8DCF5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.158 (Depositor) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33upd

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.963	α = 90
b = 153.963	β = 90
c = 153.963	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Winsor, J., Dubrovska, I., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description