5KMW | pdb_00005kmw

TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex

• PDB DOI: https://doi.org/10.2210/pdb5KMW/pdb

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


• Deposited: 2016-06-27 Released: 2017-03-01 
• Deposition Author(s): Coates, L., Langan, P.S., Vandavasi, V.G., Weiss, K.L., Cooper, J.B., Ginell, S.L.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.170 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.130 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Literature

TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex

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

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: 28.99 kDa 
• Atom Count: 2,623 
• Modelled Residue Count: 256 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase Toho-1	A	256	Escherichia coli	Mutation(s): 3  Gene Names: bla EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066  Go to UniProtKB:  Q47066

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNM	D [auth A]	OPEN FORM - PENICILLIN G C16 H20 N2 O4 S OGFZUTGOGYUTKZ-KWCYVHTRSA-N
PNN	E [auth A], F [auth A]	PENICILLIN G C16 H18 N2 O4 S JGSARLDLIJGVTE-MBNYWOFBSA-N
SO4	B [auth A], C [auth A], G [auth A], H [auth A], I [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:  0.170 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.130 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.262	α = 90
b = 72.262	β = 90
c = 98.193	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data scaling
SCALA	data scaling
Coot	model building
SHELX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Coates, L., Langan, P.S., Vandavasi, V.G., Weiss, K.L., Cooper, J.B., Ginell, S.L.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	32102548

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary