2BCO

X-ray structure of succinylglutamate desuccinalase from Vibrio Parahaemolyticus (RIMD 2210633) at the resolution 2.3 A, Northeast Structural Genomics Target Vpr14

• PDB DOI: https://doi.org/10.2210/pdb2BCO/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-19 Released: 2005-10-25 
• Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Benach, J., Zhou, W., Acton, T., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

X-ray structure of succinylglutamate desuccinalase from Vibrio Parahaemolyticus (RIMD 2210633) at the resolution 2.3 A, Northeast Structural Genomics Target Vpr14

Kuzin, A.P., Abashidze, M., Forouhar, F., Benach, J., Zhou, W., Acton, T., Xiao, R., Conover, K., Ma, L.C., Kellie, R., Cunningham, K.E., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.61 kDa 
• Atom Count: 5,393 
• Modelled Residue Count: 630 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinylglutamate desuccinylase	A, B	350	Vibrio parahaemolyticus	Mutation(s): 6  Gene Names: astE EC: 3.1 (PDB Primary Data), 3.5.1.96 (UniProt)
UniProt
Find proteins for Q87Q40 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87Q40  Go to UniProtKB:  Q87Q40

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.852	α = 90
b = 72.555	β = 105.66
c = 93.032	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Benach, J., Zhou, W., Acton, T., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary