6HUH | pdb_00006huh

CRYSTAL STRUCTURE OF OXA-427 class D BETA-LACTAMASE

• PDB DOI: https://doi.org/10.2210/pdb6HUH/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-08 Released: 2019-10-30 
• Deposition Author(s): Zavala, A., Retailleau, P., Bogaerts, P., Glupczynski, Y., Naas, T., Iorga, B.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.269 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF CMY-OXA-427-HisTag BETA-LACTAMASE

Zavala, A., Naas, T., Bogaerts, P., Glupczynski, Y., Retailleau, P., Iorga, B.I.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.29 kDa 
• Atom Count: 3,971 
• Modeled Residue Count: 484 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	274	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaOXA-427, PKLPN57_278 EC: 3.5.2.6
UniProt
Find proteins for A0A1Y6M6D7 (Klebsiella pneumoniae) Explore A0A1Y6M6D7  Go to UniProtKB:  A0A1Y6M6D7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.78 Å
• R-Value Free:  0.269 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.79	α = 90
b = 42.58	β = 114.37
c = 99.71	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Zavala, A., Retailleau, P., Bogaerts, P., Glupczynski, Y., Naas, T., Iorga, B.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-LABX-33
French National Research Agency	France	ANR-14-JAMR-0002

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description