Beta-lactamase Toho-1
Escherichia coli
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain A; UniProt 30–291 | Mutation:R274N, R276N | SO4 SULFATE ION × 5 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K | Resolution 1.03 Å R-free 0.148 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 2ZQ8 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1BZA BETA-LACTAMASE TOHO-1 FROM ESCHERICHIA COLI TUH12191 Deposited 1998-10-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
33–290(258 aa)
|
Mutation:E166A | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.5;pH 4.5
|
Resolution 1.80 Å R-free 0.217 |
| 1IYO Toho-1 beta-Lactamase In Complex With Cefotaxime Deposited 2002-09-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A | SO4 SULFATE ION × 3 CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;300 K;ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.80 Å R-free 0.206 |
| 1IYP Toho-1 beta-Lactamase In Complex With Cephalothin Deposited 2002-09-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A | SO4 SULFATE ION × 3 CEP CEPHALOTHIN GROUP × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;300 K;ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.00 Å R-free 0.245 |
| 1IYQ Toho-1 beta-Lactamase In Complex With Benzylpenicillin Deposited 2002-09-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A | SO4 SULFATE ION × 3 PNM OPEN FORM - PENICILLIN G × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;300 K;ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 2.10 Å R-free 0.227 |
| 1IYS Crystal Structure of Class A beta-Lactamase Toho-1 Deposited 2002-09-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
31–291(261 aa)
|
Not recorded | SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;ammonium sulfate, sodium acetate, acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.65 Å R-free 0.197 |
| 1WE4 Crystal Structure of Class A beta-Lactamase Toho-1 G238C mutant Deposited 2004-05-24 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:A26M, G238C | SO4 SULFATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;Ammonium sulfate, sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.70 Å R-free 0.222 |
| 2WYX Neutron structure of a class A Beta-lactamase Toho-1 E166A R274N R276N triple mutant Deposited 2009-11-20 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
33–288(256 aa)
Fragment:RESIDUES 33-288
|
Mutation:YES | No recorded non-water small molecule |
NEUTRON DIFFRACTION
X-ray crystallization conditions
pH 6.5;pH 6.5
|
Resolution 2.10 Å R-free 0.258 |
| 2XQZ Neutron structure of the perdeuterated Toho-1 R274N R276N double mutant beta-lactamase Deposited 2010-09-08 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
32–291(260 aa)
Fragment:RESIDUES 32-291
|
Mutation:YES | No recorded non-water small molecule |
NEUTRON DIFFRACTION
X-ray crystallization conditions
pH 6.5;pH 6.5
|
Resolution 2.10 Å R-free 0.259 |
| 2XR0 Room temperature X-ray structure of the perdeuterated Toho-1 R274N R276N double mutant beta-lactamase Deposited 2010-09-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
32–291(260 aa)
Fragment:RESIDUES 32-291
|
Mutation:YES | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5;2.0 A AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PD 5.1. PREPARED IN 99.9% D2O AND MIXED 1:1 WITH PERDEUTERATED PROTEIN PREPARED IN 20 MM NA MES AT PD 6.1 (PH 6.5).
|
Resolution 2.20 Å R-free 0.173 |
| 2ZQ7 Apo structure of Class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant Deposited 2008-08-07 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A, R274N, R276N | SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;1.95-2.10M Ammonium sulfate, 0.2M sodium citrate, pH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 0.94 Å R-free 0.147 |
| 2ZQ9 Cephalothin acyl-intermediate structure of class a beta-lactamase Toho-1 E166A/R274N/R276N triple mutant Deposited 2008-08-07 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A, R274N, R276N | SO4 SULFATE ION × 2 CEO 5-METHYLENE-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 CLS CEPHALOTHIN × 1 SPA THIOPHENEACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.07 Å R-free 0.146 |
| 2ZQA Cefotaxime acyl-intermediate structure of class a beta-lacta Toho-1 E166A/R274N/R276N triple mutant Deposited 2008-08-07 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A, R274N, R276N | CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 0.95 Å R-free 0.145 |
| 2ZQC Aztreonam acyl-intermediate structure of class a beta-lactam Toho-1 E166A/R274N/R276N triple mutant Deposited 2008-08-07 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A, R274N, R276N | SO4 SULFATE ION × 4 AZR 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.07 Å R-free 0.146 |
| 2ZQD Ceftazidime acyl-intermediate structure of class a beta-lact Toho-1 E166A/R274N/R276N triple mutant Deposited 2008-08-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:E166A, R274N, R276N | SO4 SULFATE ION × 4 CAZ ACYLATED CEFTAZIDIME × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;1.95-2.10M Ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.19 Å R-free 0.159 |
| 4BD0 X-ray structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB) Deposited 2012-10-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
31–291(261 aa)
Fragment:RESIDUES 32-291
|
Mutation:YES | BZB BENZO[B]THIOPHENE-2-BORONIC ACID × 1 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
293 K;2.0 M AMMONIUM SULFATE AND 0.1 M SODIUM CITRATE PD 5.1 PREPARED IN 99.9 PERCENT D2O AT 20 C
|
Resolution 1.21 Å R-free 0.133 |
| 4BD1 Neutron structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB) Deposited 2012-10-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
31–291(261 aa)
|
Mutation:YES | BZB BENZO[B]THIOPHENE-2-BORONIC ACID × 1 |
NEUTRON DIFFRACTION
X-ray crystallization conditions
pH 6.5;PH 6.5
|
Resolution 2.00 Å R-free 0.257 |
| 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 Deposited 2013-08-26 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
31–291(261 aa)
|
Mutation:YES | BZB BENZO[B]THIOPHENE-2-BORONIC ACID × 1 |
NEUTRON DIFFRACTION
X-ray crystallization conditions
pH 5.6;PH 5.6
|
Resolution 2.20 Å R-free 0.240 |
| 4X69 Crystal structure of OP0595 complexed with CTX-M-44 Deposited 2014-12-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Not recorded | OP0 (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8;293 K;PEG 6000
|
Resolution 1.42 Å R-free 0.208 |
| 4X69 Crystal structure of OP0595 complexed with CTX-M-44 Deposited 2014-12-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
30–291(262 aa)
|
Not recorded | OP0 (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8;293 K;PEG 6000
|
Resolution 1.42 Å R-free 0.208 |
| 5A91 15K X-ray ligand free: Exploring the Mechanism of beta-Lactam Ring Protonation in the Class A beta-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography Deposited 2015-07-17 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
30–291(262 aa)
|
Mutation:YES | SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
293 K;300 ul of a 10 mg/ml protein concentration in a
solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1) prepared in D 2 O.
|
Resolution 1.20 Å R-free 0.150 |
| 5KMW TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex Deposited 2016-06-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
33–288(256 aa)
|
Mutation:E165A, R271N, R273N | SO4 SULFATE ION × 5 PNM OPEN FORM - PENICILLIN G × 1 PNN PENICILLIN G × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE;pH 6.1;293.15 K;30 microliters of 10 mg/ml protein concentration was added to a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1). For ligand soaking, crystals were placed for 2-3 h in a reservoir solution containing 2.7 M ammonium sulfate, 0.1 M sodium citrate (pH 6.1), and 5.0 mM benzyl penicillin. The crystals were then placed momentarily in a reservoir solution containing a cryoprotectant (30% w/v trehalose) and subsequently flash-frozen in liquid nitrogen
|
Resolution 1.10 Å R-free 0.170 |
| 5KSC E166A/R274N/R276N Toho-1 Beta-lactamase aztreonam acyl-enzyme intermediate Deposited 2016-07-08 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
31–291(261 aa)
|
Mutation:E169A, R275N, R277N | AZR 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid × 1 |
NEUTRON DIFFRACTION
X-ray crystallization conditions
BATCH MODE;pH 6.1;293.15 K;300 microliters of a 10 mg/ml protein concentration in a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1) prepared in D2O.
|
Resolution 2.10 Å R-free 0.280 |
| 6C78 Substrate Binding Induces Conformational Changes In A Class A Beta Lactamase That Primes It For Catalysis Deposited 2018-01-22 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
32–291(260 aa)
Fragment:RESIDUES 32-291
|
Not recorded | No recorded non-water small molecule |
NEUTRON DIFFRACTION
X-ray crystallization conditions
BATCH MODE;pH 6.1;293 K;300 MICROLITERS OF A 10 MG/ML PROTEIN
CONCENTRATION IN A SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE
AND 0.1 M PREPARED IN D2O, PH 6.1, BATCH MODE, TEMPERATURE 293K
|
Resolution 1.75 Å |
| 6C79 Conformational Changes in a Class A Beta lactamase that Prime it for Catalysis Deposited 2018-01-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
32–291(260 aa)
Fragment:residues 32-291
|
Not recorded | CE3 (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 × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE;pH 6.1;293 K;10 mg/ml protein in a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1)
|
Resolution 1.10 Å R-free 0.164 |
| 6C7A Conformational Changes in a Class A Beta lactamase that Prime it for Catalysis Deposited 2018-01-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
32–291(260 aa)
Fragment:residues 32-291
|
Not recorded | SO4 SULFATE ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE;pH 6.1;293 K;10 mg/ml protein in a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1)
|
Resolution 1.05 Å R-free 0.150 |
24 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | BLT1_ECOLX |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–262; UniProt 30–291 |