3M2J | pdb_00003m2j

Crystal Structure of fluorescein-labeled Class A -lactamase PenP

• PDB DOI: https://doi.org/10.2210/pdb3M2J/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-07 Released: 2011-03-16 
• Deposition Author(s): Zhao, Y.X., Leung, Y.C., Wong, W.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.273 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of fluorescein-labeled Class A -lactamase PenP

Zhao, Y.X., Leung, Y.C., Wong, W.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 57.81 kDa 
• Atom Count: 4,303 
• Modeled Residue Count: 513 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	257	Bacillus licheniformis	Mutation(s): 1  Gene Names: penP EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808  Go to UniProtKB:  P00808

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F5M	D [auth A]	5-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid C24 H13 N O7 HFBMFFXWMZRDIY-UHFFFAOYSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.273 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.354	α = 90
b = 92.34	β = 104.84
c = 66.415	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Zhao, Y.X., Leung, Y.C., Wong, W.T.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description