2ZQ9 | pdb_00002zq9

Cephalothin acyl-intermediate structure of class a beta-lactamase Toho-1 E166A/R274N/R276N triple mutant

• PDB DOI: https://doi.org/10.2210/pdb2ZQ9/pdb

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


• Deposited: 2008-08-07 Released: 2009-07-28 
• Deposition Author(s): Nitanai, Y., Shimamura, T., Uchiyama, T., Ishii, Y., Takehira, M., Yutani, K., Matsuzawa, H., Miyano, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 
  0.146 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Extend Spectrum Beta-Lactamase in Correlation of Enzymatic Kinetics and Thermal Stability of Acyl-Intermediates

Nitanai, Y., Shimamura, T., Uchiyama, T., Ishii, Y., Takehira, M., Yutani, K., Matsuzawa, H., Miyano, M.

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: 29.19 kDa 
• Atom Count: 2,549 
• Modeled Residue Count: 259 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase Toho-1	A	262	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLS	E [auth A]	CEPHALOTHIN C16 H16 N2 O6 S2 XIURVHNZVLADCM-IUODEOHRSA-N
CEO	D [auth A]	5-METHYLENE-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID C14 H14 N2 O4 S2 FYGLCWWPHIWVKN-ZWNOBZJWSA-N
SPA	F [auth A]	THIOPHENEACETIC ACID C6 H6 O2 S SMJRBWINMFUUDS-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free:  0.146 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.421	α = 90
b = 72.421	β = 90
c = 97.518	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Nitanai, Y., Shimamura, T., Uchiyama, T., Ishii, Y., Takehira, M., Yutani, K., Matsuzawa, H., Miyano, M.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary