6NJ1 | pdb_00006nj1

Crystal structure of class A beta-lactamase from Clostridium kluyveri DSM 555

• PDB DOI: https://doi.org/10.2210/pdb6NJ1/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium kluyveri DSM 555
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-02 Released: 2019-01-16 
• Deposition Author(s): Michalska, K., Welk, L., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.151 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Literature

Crystal structure of class A beta-lactamase from Clostridium kluyveri DSM 555

Michalska, K., Welk, L., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 31.14 kDa 
• Atom Count: 2,266 
• Modeled Residue Count: 262 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	282	Clostridium kluyveri DSM 555	Mutation(s): 0  Gene Names: bla, CKL_2902 EC: 3.5.2.6
UniProt
Find proteins for A5N1B8 (Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NBRC 12016 / NCIMB 10680 / K1)) Explore A5N1B8  Go to UniProtKB:  A5N1B8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.151 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36nj1

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.878	α = 90
b = 66.878	β = 90
c = 119.795	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Michalska, K., Welk, L., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary