2PVA

OXIDIZED PENICILLIN V ACYLASE FROM B. SPHAERICUS

• PDB DOI: https://doi.org/10.2210/pdb2PVA/pdb

• Classification: HYDROLASE
• Organism(s): Lysinibacillus sphaericus
• Mutation(s): Yes 


• Deposited: 1998-11-13 Released: 2000-07-26 
• 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: 2.50 Å
• R-Value Free: 0.245 
• R-Value Work: 0.196 

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 (software)

Macromolecule Content

• Total Structure Weight: 153.93 kDa 
• Atom Count: 11,209 
• Modelled Residue Count: 1,328 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN V ACYLASE	A, B, C, D	345	Lysinibacillus sphaericus	Mutation(s): 1  EC: 3.5.1.11
UniProt
Find proteins for P12256 (Lysinibacillus sphaericus) Explore P12256  Go to UniProtKB:  P12256

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTD	E [auth A], F [auth B], G [auth C], H [auth D]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.245 
• R-Value Work: 0.196 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.4	α = 90
b = 208.4	β = 90
c = 96.2	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-07-26 
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: 2000-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-11
  Changes: Data collection, Database references
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations