4PEM | pdb_00004pem

Crystal Structure of S1G mutant of Penicillin G Acylase from Kluyvera citrophila

• PDB DOI: https://doi.org/10.2210/pdb4PEM/pdb

• Classification: HYDROLASE
• Organism(s): Kluyvera cryocrescens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2014-04-24 Released: 2015-07-22 
• Deposition Author(s): Ramasamy, S., Varshney, N.K., Brannigan, J.A., Wilkinson, A.J., Suresh, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of S1G mutant of Penicillin G Acylase from Kluyvera citrophilla

Varshney, N.K., Ramasamy, S., Brannigan, J.A., Wilkinson, A.J., Suresh, C.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 379.84 kDa 
• Atom Count: 25,838 
• Modeled Residue Count: 3,238 
• Deposited Residue Count: 3,416 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase Alpha	A, C, E, G	286	Kluyvera cryocrescens	Mutation(s): 0
UniProt
Find proteins for A0A068F6N5 (Kluyvera cryocrescens) Explore A0A068F6N5  Go to UniProtKB:  A0A068F6N5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase Beta	B, D, F, H	568	Kluyvera cryocrescens	Mutation(s): 1
UniProt
Find proteins for A0A068F6N5 (Kluyvera cryocrescens) Explore A0A068F6N5  Go to UniProtKB:  A0A068F6N5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54	α = 104.05
b = 124.561	β = 101.37
c = 135.139	γ = 96.51

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Ramasamy, S., Varshney, N.K., Brannigan, J.A., Wilkinson, A.J., Suresh, C.G.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy