8de2

TEM-1 beta-lactamase A237Y mutant covalently bound to avibactam, a room temperature structure

Method: X-RAY DIFFRACTION Dmax: 115.7 Å Quality: GOOD

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

Beta-lactamase TEM

Escherichia coli

UniProt P62593

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 24–286 Mutation:M182T, A237Y NXL (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;296 K;PEG3350, HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) Resolution 2.45 Å R-free 0.249
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 24–286 Mutation:M182T, A237Y NXL (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;296 K;PEG3350, HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) Resolution 2.45 Å R-free 0.249
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 24–286 Mutation:M182T, A237Y NXL (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;296 K;PEG3350, HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) Resolution 2.45 Å R-free 0.249
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 24–286 Mutation:M182T, A237Y NXL (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;296 K;PEG3350, HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) Resolution 2.45 Å R-free 0.249

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.

72 other PDB entries and 152 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLAT_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–264; UniProt 24–286 Author chain B; PDBConstruct 2–264; UniProt 24–286 Author chain C; PDBConstruct 2–264; UniProt 24–286 Author chain D; PDBConstruct 2–264; UniProt 24–286

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 8de2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8de2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8de2
Deposition date deposition_date2022-06-19
Structure title titleTEM-1 beta-lactamase A237Y mutant covalently bound to avibactam, a room temperature structure
Keywords keywordsHydrolase, Beta-lactamase, TEM, avibactam, room-temperature, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.89
Radius of gyration Rg (electron density) rg_electron35.73
Forward intensity I(0) i0219025000.00
Molecular weight molecular_weight116920.0 kDa
Excluded volume excluded_volume145450 ų
Envelope volume envelope_volume184420 ų
Hydration-shell volume shell_volume45201 ų
Envelope diameter envelope_diameter124.3
Shell Rg shell_rg40.07
Envelope Rg envelope_rg35.52
Shape Rg shape_rg35.75
Total Rg total_rg35.93
Total atoms total_atoms8200
Residues n_residues1052
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 dmax115.7
Rg (real space) rg_real36.13
Rg uncertainty (real space) rg_real_error1.04
I(0) (real space) i0_real2.1900e+08
I(0) uncertainty (real space) i0_real_error4.0490e+06
Rg (reciprocal space) rg_reciprocal35.98
I(0) (reciprocal space) i0_reciprocal219000000.0000
Solution quality estimate total_estimate0.8247
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.4
Skewness Skewness skewness0.557
Kurtosis Kurtosis kurtosis-0.116
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56100000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.172

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)