6C79

Conformational Changes in a Class A Beta lactamase that Prime it for Catalysis

• PDB DOI: https://doi.org/10.2210/pdb6C79/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-22 Released: 2018-03-21 
• Deposition Author(s): Coates, L., Langan, P.S., Vandavasi, V.G., Cooper, S.J., Weiss, K.L., Ginell, S.L., Parks, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.164 
• R-Value Work: 0.144 

Literature

Substrate Binding Induces Conformational Changes in a Class A Beta-lactamase That Prime It for Catalysis

Langan, P.S., Vandavasi, V.G., Cooper, S.J., Weiss, K.L., Ginell, S.L., Parks, J.M., Coates, L.

(2018) ACS Catal 8: 2428-2437

• DOI: https://doi.org/10.1021/acscatal.7b04114

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: 28.89 kDa 
• Atom Count: 2,446 
• Modelled Residue Count: 260 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase Toho-1	A	261	Escherichia coli	Mutation(s): 0  Gene Names: bla EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066  Go to UniProtKB:  Q47066

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CE3	B [auth A]	(6R,7R)-3-(acetyloxymethyl)-7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-8-oxo-5-thia-1-azabicy clo[4.2.0]oct-2-ene-2-carboxylic acid C16 H17 N5 O7 S2 GPRBEKHLDVQUJE-QSWIMTSFSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.164 
• R-Value Work: 0.144 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.72	α = 90
b = 72.72	β = 90
c = 98.944	γ = 120

Software Package:

Software Name	Purpose
SHELXL	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Coates, L., Langan, P.S., Vandavasi, V.G., Cooper, S.J., Weiss, K.L., Ginell, S.L., Parks, J.M.

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Refinement description
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Structure summary