3BR8

Crystal structure of acylphosphatase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3BR8/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-21 Released: 2008-06-24 
• Deposition Author(s): Li, D., Hu, J.C., Xia, B., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.225 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Conformational Transitions Revealed by Structures of Acylphosphatase from Bacillus subtilis in Different States

Hu, J.C., Li, D., Su, X.D., Jin, C.W., Xia, B.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 10.52 kDa 
• Atom Count: 828 
• Modelled Residue Count: 90 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable acylphosphatase	A	91	Bacillus subtilis	Mutation(s): 0  Gene Names: yflL EC: 3.6.1.7
UniProt
Find proteins for O35031 (Bacillus subtilis (strain 168)) Explore O35031  Go to UniProtKB:  O35031

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.225 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.857	α = 90
b = 48.27	β = 90
c = 59.567	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Li, D., Hu, J.C., Xia, B., Su, X.D.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations