4HL1

Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin

• PDB DOI: https://doi.org/10.2210/pdb4HL1/pdb

• Classification: Hydrolase/Antibiotic
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-10-15 Released: 2012-12-12 
• Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Mire, J., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.149 
• R-Value Work: 0.137 
• R-Value Observed: 0.137 

Starting Model: experimental

Literature

Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin

Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Mire, J., Sacchettini, J., Joachimiak, A.

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: 52.92 kDa 
• Atom Count: 4,327 
• Modelled Residue Count: 478 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase NDM-1	A, B	243	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaNDM-1 EC: 3.5.2.6
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
ZZ7	C [auth A], H [auth B]	(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C16 H21 N3 O5 S KDAWOPKDXRJNHV-MPPDQPJWSA-N
CD	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	G [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.149 
• R-Value Work: 0.137 
• R-Value Observed: 0.137 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M34HL1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.997	α = 90
b = 78.7	β = 90
c = 134.377	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Mire, J., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description