6MGZ

Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6MGZ/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• 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: 0.179 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 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.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.09 kDa 
• Atom Count: 3,790 
• Modelled Residue Count: 458 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NDM-4	A, B	243	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaNDM-4
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422  Go to UniProtKB:  C7C422

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], O [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.182	α = 90
b = 78.977	β = 90
c = 131.08	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