3E0K | pdb_00003e0k

Crystal structure of C-termianl domain of N-acetylglutamate synthase from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3E0K/pdb

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


• Deposited: 2008-07-31 Released: 2008-08-19 
• Deposition Author(s): Chang, C., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.254 (Depositor) 
• R-Value Work: 
  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal structure of C-termianl domain of N-acetylglutamate synthase from Vibrio parahaemolyticus

Chang, C., Shackelford, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 17.51 kDa 
• Atom Count: 1,239 
• Modeled Residue Count: 146 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino-acid acetyltransferase	A	150	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: argA, VP2371 EC: 2.3.1.1
UniProt
Find proteins for Q87M87 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87M87  Go to UniProtKB:  Q87M87

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.254 (Depositor) 
• R-Value Work:  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.232	α = 90
b = 64.232	β = 90
c = 112.718	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Chang, C., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary