1YW4 | pdb_00001yw4

Crystal Structure of the Succinylglutamate Desuccinylase from Chromobacterium violaceum, Northeast Structural Genomics Target CvR22.

• PDB DOI: https://doi.org/10.2210/pdb1YW4/pdb

• Classification: HYDROLASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-17 Released: 2005-03-01 
• Deposition Author(s): Forouhar, F., Abashidze, M., Conover, K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.262 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal Structure of the Succinylglutamate Desuccinylase from Chromobacterium violaceum, Northeast Structural Genomics Target CvR22.

Forouhar, F., Abashidze, M., Conover, K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

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.

Macromolecule Content

• Total Structure Weight: 75.87 kDa 
• Atom Count: 5,277 
• Modelled Residue Count: 628 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinylglutamate desuccinylase	A, B	341	Chromobacterium violaceum ATCC 12472	Mutation(s): 5  Gene Names: astE EC: 3.1 (PDB Primary Data), 3.5.1.96 (UniProt)
UniProt
Find proteins for Q7NU26 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NU26  Go to UniProtKB:  Q7NU26

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: 2.00 Å
• R-Value Free:  0.262 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.95	α = 90
b = 39.435	β = 94.74
c = 131.585	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Forouhar, F., Abashidze, M., Conover, K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary