2ZQ8 | pdb_00002zq8

Apo structure of class a beta-lactamase Toho-1 R274N/R276N double mutant

• PDB DOI: https://doi.org/10.2210/pdb2ZQ8/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): Shimamura, T., Nitanai, Y., Uchiyama, T., Ago, H., Matsuzawa, H., Miyano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Improvement of crystal quality by surface mutations of beta-lactamase Toho-1

Shimamura, T., Nitanai, Y., Uchiyama, T., Matsuzawa, H.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 379-382

• PubMed: 19342785 
• DOI: https://doi.org/10.1107/S1744309109008240
• Primary Citation Related Structures: 
  2ZQ8


• PubMed Abstract: 
  

  The beta-lactamase Toho-1 exhibits a strong tendency to form merohedrally twinned crystals. Here, the crystal quality of Toho-1 was improved by using surface modification to remove a sulfate ion involved in crystal packing. The surface-modified Toho-1 variant (R274N/R276N) was crystallized under similar conditions to those used for wild-type Toho-1. R274N/R276N did not form merohedrally twinned crystals. The crystals diffracted to a significantly higher resolution (approximately 0.97 A) than the wild-type crystals (1.65 A); they belonged to the same space group and had almost identical unit-cell parameters to those of wild-type Toho-1.

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Organizational Affiliation: 
• RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan. [e-mail]

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: 28.66 kDa 
• Atom Count: 2,733 
• Modeled Residue Count: 261 
• 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): 2  Gene Names: bla EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066  Go to UniProtKB:  Q47066

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], 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: 1.03 Å
• R-Value Free:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.511	α = 90
b = 72.511	β = 90
c = 97.477	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Shimamura, T., Nitanai, Y., Uchiyama, T., Ago, H., 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