3PVA

PENICILLIN V ACYLASE FROM B. SPHAERICUS

• PDB DOI: https://doi.org/10.2210/pdb3PVA/pdb

• Classification: HYDROLASE
• Organism(s): Lysinibacillus sphaericus
• Mutation(s): No 


• Deposited: 1998-11-13 Released: 1999-11-15 
• Deposition Author(s): Suresh, C.G., Pundle, A.V., Rao, K.N., Sivaraman, H., Brannigan, J.A., Mcvey, C.E., Verma, C.S., Dauter, Z., Dodson, E.J., Dodson, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 

Starting Model: experimental

Literature

Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members.

Suresh, C.G., Pundle, A.V., SivaRaman, H., Rao, K.N., Brannigan, J.A., McVey, C.E., Verma, C.S., Dauter, Z., Dodson, E.J., Dodson, G.G.

(1999) Nat Struct Biol 6: 414-416

• PubMed: 10331865 
• DOI: https://doi.org/10.1038/8213
• Primary Citation of Related Structures:  
  2PVA, 3PVA

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Organizational Affiliation: 

Division of Biochemical Sciences, National Chemical Laboratory, Pune, India. [e-mail]

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,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 297.51 kDa 
• Atom Count: 23,640 
• Modelled Residue Count: 2,672 
• Deposited Residue Count: 2,680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PENICILLIN V ACYLASE)	A, B, C, D, E, F, G, H	335	Lysinibacillus sphaericus	Mutation(s): 0  EC: 3.5.1.11
UniProt
Find proteins for P12256 (Lysinibacillus sphaericus) Explore P12256  Go to UniProtKB:  P12256

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.4	α = 88.3
b = 129.6	β = 83.4
c = 156.7	γ = 84.6

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-15 
Deposition Author(s): Suresh, C.G., Pundle, A.V., Rao, K.N., Sivaraman, H., Brannigan, J.A., Mcvey, C.E., Verma, C.S., Dauter, Z., Dodson, E.J., Dodson, G.G.

Revision History  

• Version 1.0: 1999-11-15
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description