4C3Q

Neutron structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB) at 100K

PDB DOI: https://doi.org/10.2210/pdb4C3Q/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli BL21
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2013-08-26 Released: 2014-07-09
Deposition Author(s): Coates, L., Tomanicek, S.J., Schrader, T., Weiss, K.L., Ng, J.D., Ostermann, A.

Experimental Data Snapshot

Method: NEUTRON DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240
R-Value Work: 0.192
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryogenic Neutron Protein Crystallography: Routine Methods and Potential Benefits

Coates, L., Tomanicek, S.J., Schrader, T., Weiss, K.L., Ng, J.D., Ostermann, A.

(2014) J Appl Crystallogr 47

DOI: https://doi.org/10.1107/S1600576714010772

Macromolecule Content

Total Structure Weight: 28.28 kDa
Atom Count: 2,107
Modelled Residue Count: 261
Deposited Residue Count: 261
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE TOHO-1	A	261	Escherichia coli BL21	Mutation(s): 2 EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066 Go to UniProtKB: Q47066
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q47066
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BZB Query on BZB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	BENZO[B]THIOPHENE-2-BORONIC ACID C₈ H₇ B O₂ S YNCYPMUJDDXIRH-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: NEUTRON DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.889	α = 90
b = 72.889	β = 90
c = 98.189	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Tomanicek, S.J.

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2017-03-22
Changes: Atomic model, Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.