1K6S | pdb_00001k6s

STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEX WITH A PHENYLBORONIC ACID

• PDB DOI: https://doi.org/10.2210/pdb1K6S/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-10-17 Released: 2003-06-24 
• Deposition Author(s): Kerff, F., Fonze, E., Sauvage, E., Frere, J.M., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF CLASS D BETA-LACTAMASE OXA-10 IN COMPLEX WITH DIFFERENT SUBSTRATES AND ONE INHIBITOR.

Kerff, F., Fonze, E., Sauvage, E., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.34 kDa 
• Atom Count: 4,192 
• Modeled Residue Count: 489 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase PSE-2	A, B	248	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: plasmid pMON234 EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa) Explore P14489  Go to UniProtKB:  P14489

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IAP	F [auth A], H [auth B]	4-IODO-ACETAMIDO PHENYLBORONIC ACID C8 H9 B I N O3 LMHXPDZPXBIIEX-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A], D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.03 Å
• R-Value Free:  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.245	α = 90
b = 95.787	β = 90
c = 125.074	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., Sauvage, E., 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: 2022-12-21
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary