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 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

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