SAXSdb — 5kmw

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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 33–288	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

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 5KMW	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 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 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 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 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 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 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 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 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 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 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
2ZQ8 Apo structure of class a beta-lactamase Toho-1 R274N/R276N double mutant Deposited 2008-08-07	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 30–291（262 aa）	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
2ZQ9 Cephalothin acyl-intermediate structure of class a beta-lactamase Toho-1 E166A/R274N/R276N triple mutant Deposited 2008-08-07	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 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 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 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 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 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 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 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 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 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 construct 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 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 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
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 1–256； UniProt 33–288

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5kmw
Deposition date deposition_date	2016-06-27
Structure title title	TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex
Keywords keywords	Class A beta-lactamase, substrate recognition, acyl-enzyme, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.92 Å
Radius of gyration Rg (electron density) rg_electron	17.61 Å
Forward intensity I(0) i0	15802100.00
Molecular weight molecular_weight	28942.0 kDa
Excluded volume excluded_volume	35824 Å³
Envelope volume envelope_volume	40105 Å³
Hydration-shell volume shell_volume	18724 Å³
Envelope diameter envelope_diameter	63.6 Å
Shell Rg shell_rg	24.40 Å
Envelope Rg envelope_rg	18.15 Å
Shape Rg shape_rg	17.59 Å
Total Rg total_rg	18.65 Å
Total atoms total_atoms	2023
Residues n_residues	256
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	61.9 Å
Rg (real space) rg_real	18.83 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.5800e+07
I(0) uncertainty (real space) i0_real_error	1.8690e+05
Rg (reciprocal space) rg_reciprocal	18.85 Å
I(0) (reciprocal space) i0_reciprocal	15800000.0000
Solution quality estimate total_estimate	0.6606
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.233
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3424000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 0.999; Sysdev: 0.374; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase Toho-1
Molecular weight formula_weight	27503.1 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	E165A, R271N, R273N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2623

VQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTAPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAENRNDILAAAAKIVT

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	OPEN FORM - PENICILLIN G
Molecular weight formula_weight	336.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PENICILLIN G
Molecular weight formula_weight	334.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	516

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5kmwa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id	5kmwA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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8. Citations (1)

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Unit-cell length a length_a	72.262 Å
Unit-cell length b length_b	72.262 Å
Unit-cell length c length_c	98.193 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1360
R_work r_work	—
R_free r_free	0.1700

fit	/app/data/saxs_computation/km/5kmw/5kmw.fit
pddf	/app/data/pr_computation/km/5kmw/5kmw.pr.out
profile	/app/data/saxs_computation/km/5kmw/5kmw.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-lactamase Toho-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction