2OQC | pdb_00002oqc

Crystal Structure of Penicillin V acylase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2OQC/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-31 Released: 2008-01-15 
• Deposition Author(s): Suresh, C.G., Rathinaswamy, P., Pundle, A.V., Prabhune, A.A., Sivaraman, H., Brannigan, J.A., Dodson, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Penicillin V acylase from Bacillus subtilis

Suresh, C.G., Rathinaswamy, P., Pundle, A.V., Prabhune, A.A., Sivaraman, H., Brannigan, J.A., Dodson, G.G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 74.08 kDa 
• Atom Count: 5,502 
• Modeled Residue Count: 634 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin V acylase	A, B	327	Bacillus subtilis	Mutation(s): 0  Gene Names: yxeI EC: 3.5.1.11
UniProt
Find proteins for P54948 (Bacillus subtilis (strain 168)) Explore P54948  Go to UniProtKB:  P54948

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.963	α = 90
b = 307.956	β = 90
c = 56.003	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Suresh, C.G., Rathinaswamy, P., Pundle, A.V., Prabhune, A.A., Sivaraman, H., Brannigan, J.A., Dodson, G.G.

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2014-04-16
  Changes: Other
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description