4rx2

A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis

Method: X-RAY DIFFRACTION Dmax: 135.3 Å Quality: REASONABLE

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 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 24–286 Fragment:TEM-1 beta-lactamase Mutation:W165Y/E166Y/P167G/M182T SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.268

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 148 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 1–263; UniProt 24–286 Author chain B; PDBConstruct 1–263; UniProt 24–286 Author chain C; PDBConstruct 1–263; UniProt 24–286 Author chain D; PDBConstruct 1–263; UniProt 24–286 Author chain E; PDBConstruct 1–263; UniProt 24–286 Author chain F; PDBConstruct 1–263; UniProt 24–286 Author chain G; PDBConstruct 1–263; UniProt 24–286 Author chain H; PDBConstruct 1–263; 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 4rx2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rx2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4rx2
Deposition date deposition_date2014-12-08
Structure title titleA triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis
Keywords keywordsglobular, beta-lactamase, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.57
Radius of gyration Rg (electron density) rg_electron41.97
Forward intensity I(0) i0776004000.00
Molecular weight molecular_weight224230.0 kDa
Excluded volume excluded_volume279150 ų
Envelope volume envelope_volume368660 ų
Hydration-shell volume shell_volume72532 ų
Envelope diameter envelope_diameter143.9
Shell Rg shell_rg47.94
Envelope Rg envelope_rg41.03
Shape Rg shape_rg41.99
Total Rg total_rg42.21
Total atoms total_atoms15719
Residues n_residues2036
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 dmax135.3
Rg (real space) rg_real43.25
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real7.6470e+08
I(0) uncertainty (real space) i0_real_error9.8960e+06
Rg (reciprocal space) rg_reciprocal42.57
I(0) (reciprocal space) i0_reciprocal776100000.0000
Solution quality estimate total_estimate0.7070
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.9
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.233
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha2.0330
Highest regularization parameter α highest_alpha67740000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 0.925; Sysdev: 0.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.699

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4rx2a_
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
Domain ID domain_idd4rx2b_
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
Domain ID domain_idd4rx2c_
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
Domain ID domain_idd4rx2d_
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
Domain ID domain_idd4rx2e_
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
Domain ID domain_idd4rx2f_
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
Domain ID domain_idd4rx2g_
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
Domain ID domain_idd4rx2h_
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 (8 domains)

Domain ID domain_id4rx2A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2E00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2F00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2G00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id4rx2H00
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)