3MJI

Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor

• PDB DOI: https://doi.org/10.2210/pdb3MJI/pdb

• Classification: HYDROLASE
• Organism(s): Lysinibacillus sphaericus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-12 Released: 2011-07-20 
• Deposition Author(s): Pathak, M.C., Suresh, C.G., Dodson, G.G., Murshudov, G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor

Pathak, M.C., Suresh, C.G., Dodson, G.G., Murshudov, G.N.

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: 150.12 kDa 
• Atom Count: 10,729 
• Modelled Residue Count: 1,334 
• Deposited Residue Count: 1,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin acylase	A, B, C, D	338	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: 2.50 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.642	α = 90
b = 90.089	β = 102.13
c = 102.269	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Pathak, M.C., Suresh, C.G., Dodson, G.G., Murshudov, G.N.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references