1VPM | pdb_00001vpm

Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VPM/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-11 Released: 2004-12-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.197 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 58.77 kDa 
• Atom Count: 3,951 
• Modeled Residue Count: 460 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acyl-CoA hydrolase	A, B, C	169	Halalkalibacterium halodurans C-125	Mutation(s): 4  Gene Names: BH0798 EC: 3.1.2
UniProt
Find proteins for Q9KEQ1 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KEQ1  Go to UniProtKB:  Q9KEQ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	D [auth A], F [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PO4	E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 1.66 Å
• R-Value Free:  0.197 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VPM

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.984	α = 90
b = 106.507	β = 90
c = 120.254	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELX	model building
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing
SHARP	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary