4bd1

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

Method: NEUTRON DIFFRACTION Dmax: 64.8 Å Quality: REASONABLE

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

TOHO-1 BETA-LACTAMASE

ESCHERICHIA COLI BL21

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 31–291 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

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 1–261; UniProt 31–291

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 4bd1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4bd1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4bd1
Deposition date deposition_date2012-10-04
Structure title titleNeutron structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB)
Keywords keywordsHYDROLASE, PERDEUTERATED NEUTRON STRUCTURE, EXTENDED-SPECTRUM BETA LACTAMASES, CTX- M-TYPE ESBLS; HYDROLASE
Experimental Method methodNEUTRON DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.26
Radius of gyration Rg (electron density) rg_electron18.00
Forward intensity I(0) i06890680.00
Molecular weight molecular_weight35034.0 kDa
Excluded volume excluded_volume48988 ų
Envelope volume envelope_volume49334 ų
Hydration-shell volume shell_volume21442 ų
Envelope diameter envelope_diameter65.2
Shell Rg shell_rg25.78
Envelope Rg envelope_rg19.13
Shape Rg shape_rg18.06
Total Rg total_rg19.40
Total atoms total_atoms4365
Residues n_residues261
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 dmax64.8
Rg (real space) rg_real20.14
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real6.8910e+06
I(0) uncertainty (real space) i0_real_error8.9860e+04
Rg (reciprocal space) rg_reciprocal20.17
I(0) (reciprocal space) i0_reciprocal6891000.0000
Solution quality estimate total_estimate0.6167
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.146
Kurtosis Kurtosis kurtosis-0.267
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1491000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 0.998; Sysdev: 0.193; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4bd1a_
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_id4bd1A00
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)