2zq9

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

Method: X-RAY DIFFRACTION Dmax: 64.9 Å Quality: GOOD

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

Beta-lactamase Toho-1

Escherichia coli

UniProt Q47066

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: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

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.

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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2zq9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zq9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2zq9
Deposition date deposition_date2008-08-07
Structure title titleCephalothin acyl-intermediate structure of class a beta-lactamase Toho-1 E166A/R274N/R276N triple mutant
Keywords keywordsEXTENDED-SPECTRUM, ESBL, BETA-LACTAMASE, ACYL-ENZYME, COMPLEX, CEPHALOTHIN, TOHO-1, HYDROLASE, Antibiotic resistance, Plasmid; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.75
Radius of gyration Rg (electron density) rg_electron17.62
Forward intensity I(0) i014947400.00
Molecular weight molecular_weight28281.0 kDa
Excluded volume excluded_volume35101 ų
Envelope volume envelope_volume39233 ų
Hydration-shell volume shell_volume18441 ų
Envelope diameter envelope_diameter64.0
Shell Rg shell_rg24.11
Envelope Rg envelope_rg18.09
Shape Rg shape_rg17.62
Total Rg total_rg18.54
Total atoms total_atoms1982
Residues n_residues259
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax64.9
Rg (real space) rg_real18.66
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real1.4950e+07
I(0) uncertainty (real space) i0_real_error1.9010e+05
Rg (reciprocal space) rg_reciprocal18.68
I(0) (reciprocal space) i0_reciprocal14950000.0000
Solution quality estimate total_estimate0.8572
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1
Skewness Skewness skewness0.257
Kurtosis Kurtosis kurtosis-0.236
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3235000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.722; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2zq9a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id2zq9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily

8. Citations (1)

9. Files and Curves (10)