6NC5

Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif

• PDB DOI: https://doi.org/10.2210/pdb6NC5/pdb

• Classification: HYDROLASE
• Organism(s): Cronobacter sakazakii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-12-10 Released: 2019-12-25 
• Deposition Author(s): Monteiro Pedroso, M., Waite, D., Natasa, M., McGeary, R., Guddat, L., Hugenholtz, P., Schenk, G.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6DQH

Literature

Broad spectrum antibiotic-degrading metallo-beta-lactamases are phylogenetically diverse.

Pedroso, M.M., Waite, D.W., Melse, O., Wilson, L., Mitic, N., McGeary, R.P., Antes, I., Guddat, L.W., Hugenholtz, P., Schenk, G.

(2020) Protein Cell 11: 613-617

• PubMed: 32542533 
• DOI: https://doi.org/10.1007/s13238-020-00736-4
• Primary Citation of Related Structures:  
  6NC5

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Organizational Affiliation: 

School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Brisbane, 4072, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 28.93 kDa 
• Atom Count: 2,163 
• Modelled Residue Count: 259 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	260	Cronobacter sakazakii	Mutation(s): 2  Gene Names: CSK29544_03680

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.468	α = 90
b = 74.946	β = 90
c = 76.095	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data reduction
PHENIX	phasing
XDS	data scaling

Structure Validation

Currently 6NC5 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Monteiro Pedroso, M., Waite, D., Natasa, M., McGeary, R., Guddat, L., Hugenholtz, P., Schenk, G.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP108477
Australian Research Council (ARC)	Australia	DP150104358
Australian Research Council (ARC)	Australia	T120100694

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references
• Version 1.2: 2020-07-01
  Changes: Database references
• Version 1.3: 2020-08-05
  Changes: Database references, Derived calculations
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description