6MH0

Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6MH0/pdb

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


• Deposited: 2018-09-16 Released: 2018-10-03 
• Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, G., 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: 1.65 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 from Klebsiella pneumoniae

Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.17 kDa 
• Atom Count: 3,770 
• Modelled Residue Count: 464 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase NDM-3	A, B	243	Escherichia coli	Mutation(s): 0  Gene Names: NDM-3, blaNDM-3
UniProt
Find proteins for I3VKD5 (Escherichia coli) Explore I3VKD5  Go to UniProtKB:  I3VKD5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.185	α = 90
b = 78.699	β = 90
c = 130.79	γ = 90

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: 2018-10-03 
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, G., 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	--

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations