1K38 | pdb_00001k38

CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-2

• PDB DOI: https://doi.org/10.2210/pdb1K38/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-10-02 Released: 2003-06-24 
• Deposition Author(s): Kerff, F., Fonze, E., Bouillenne, F., Frere, J.M., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-2

Kerff, F., Fonze, E., Bouillenne, F., Frere, J.M., Charlier, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.03 kDa 
• Atom Count: 4,272 
• Modeled Residue Count: 474 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase OXA-2	A, B	254	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1  Gene Names: oxa-2 EC: 3.5.2.6
UniProt
Find proteins for P0A1V8 (Salmonella typhimurium) Explore P0A1V8  Go to UniProtKB:  P0A1V8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth B], E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.190 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.979	α = 90
b = 106.899	β = 90
c = 129.168	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-24 
Deposition Author(s): Kerff, F., Fonze, E., Bouillenne, F., Frere, J.M., Charlier, P.

Revision History  

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection