1iyp

Toho-1 beta-Lactamase In Complex With Cephalothin

Method: X-RAY DIFFRACTION Dmax: 63.2 Å Quality: GOOD

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

Toho-1 beta-lactamase

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 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

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_ECOLI
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 1iyp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1iyp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1iyp
Deposition date deposition_date2002-09-04
Structure title titleToho-1 beta-Lactamase In Complex With Cephalothin
Keywords keywordsbeta-lactamase, acyl-enzyme, complex, cephalothin, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.78
Radius of gyration Rg (electron density) rg_electron17.67
Forward intensity I(0) i015306100.00
Molecular weight molecular_weight28615.0 kDa
Excluded volume excluded_volume35491 ų
Envelope volume envelope_volume39444 ų
Hydration-shell volume shell_volume18555 ų
Envelope diameter envelope_diameter62.5
Shell Rg shell_rg24.23
Envelope Rg envelope_rg18.01
Shape Rg shape_rg17.68
Total Rg total_rg18.57
Total atoms total_atoms2004
Residues n_residues260
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 dmax63.2
Rg (real space) rg_real18.69
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real1.5310e+07
I(0) uncertainty (real space) i0_real_error1.9690e+05
Rg (reciprocal space) rg_reciprocal18.70
I(0) (reciprocal space) i0_reciprocal15310000.0000
Solution quality estimate total_estimate0.7880
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.252
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3192000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.753; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1iypa_
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_id1iypA00
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)