2GVH | pdb_00002gvh

Crystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTERIUM TUMEFACIENS at 2.65 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2GVH/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-02 Released: 2006-05-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTERIUM TUMEFACIENS at 2.65 A resolution

Joint Center for Structural Genomics (JCSG)

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: 95.91 kDa 
• Atom Count: 5,444 
• Modeled Residue Count: 748 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_L_2016p	A, B, C	288	Agrobacterium fabrum str. C58	Mutation(s): 9  Gene Names: 15159470 EC: 3.1.2.20
UniProt
Find proteins for Q7CTE6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CTE6  Go to UniProtKB:  Q7CTE6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32GVH

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.209	α = 90
b = 121.209	β = 90
c = 81.844	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-05-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary