2Z71

Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V

• PDB DOI: https://doi.org/10.2210/pdb2Z71/pdb

• Classification: HYDROLASE
• Organism(s): Lysinibacillus sphaericus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-08-10 Released: 2008-08-26 
• Deposition Author(s): Pathak, M.C., Brannigan, J., Dodson, G.G., Suresh, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 

Starting Model: experimental

Literature

Studies on the catalysis and post translational processing of penicillin V acylase

Pathak, M.C., Brannigan, J., Dodson, G.G., Suresh, C.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)

Macromolecule Content

• Total Structure Weight: 75.1 kDa 
• Atom Count: 5,260 
• Modelled Residue Count: 661 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin acylase	A, B [auth C]	335	N/A	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
PNV	C [auth A], D [auth C]	(2S,5R,6R)-3,3-DIMETHYL-7-OXO-6-(2-PHENOXYACETAMIDO)-4-THIA-1- AZABICYCLO(3.2.0)HEPTANE-2-CARBOXYLIC ACID C16 H18 N2 O5 S BPLBGHOLXOTWMN-MBNYWOFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.239 
• R-Value Observed: 0.240 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.73	α = 90
b = 158.89	β = 90
c = 90.742	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Pathak, M.C., Brannigan, J., Dodson, G.G., Suresh, C.G.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description