4GYU | pdb_00004gyu

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb4GYU/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-09-05 Released: 2012-09-26 
• Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Binkowski, T.A., 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: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae

Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Binkowski, T.A., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.5 kDa 
• Atom Count: 1,982 
• Modeled Residue Count: 241 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase NDM-1	A	243	Klebsiella pneumoniae	Mutation(s): 1  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	B [auth A], C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GYU

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.473	α = 90
b = 101.473	β = 90
c = 42.679	γ = 120

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: 2012-09-26 
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Binkowski, T.A., 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: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description