6DN4 | pdb_00006dn4

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

• PDB DOI: https://doi.org/10.2210/pdb6DN4/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Cronobacter sakazakii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-06 Released: 2019-06-12 
• 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: 1.99 Å
• R-Value Free: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6DQH 6DR8

Literature

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

Monteiro Pedroso, M., Waite, D., Melse, O., Wilson, L., Natasa, M., McGeary, R., Antes, I., Guddat, L., Hugenholtz, P., Schenk, G.

(2020) Protein Cell 

• DOI: https://doi.org/10.1007/s13238-020-00736-4

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: 32.07 kDa 
• Atom Count: 2,461 
• Modeled Residue Count: 275 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	295	Cronobacter sakazakii	Mutation(s): 0  Gene Names: CSK29544_03680

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.58	α = 90
b = 84.58	β = 90
c = 74.982	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
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: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2020-06-24
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description