4ibx

Crystal structure of stabilized TEM-1 beta-lactamase variant v.13

Method: X-RAY DIFFRACTION Dmax: 143.8 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:A42G, N52A, I84V, R120G, M182T, L201A, T265M CA CALCIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;9%(wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.68 Å R-free 0.265
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 24–286 Mutation:A42G, N52A, I84V, R120G, M182T, L201A, T265M MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;9%(wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.68 Å R-free 0.265
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 24–286 Mutation:A42G, N52A, I84V, R120G, M182T, L201A, T265M CA CALCIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;9%(wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.68 Å R-free 0.265
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 24–286 Mutation:A42G, N52A, I84V, R120G, M182T, L201A, T265M MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;9%(wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.68 Å R-free 0.265
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 24–286 Mutation:A42G, N52A, I84V, R120G, M182T, L201A, T265M No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;9%(wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.68 Å R-free 0.265

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 151 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

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 4ibx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4ibx
Deposition date deposition_date2012-12-09
Structure title titleCrystal structure of stabilized TEM-1 beta-lactamase variant v.13
Keywords keywordsTEM-1 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_guinier42.41
Radius of gyration Rg (electron density) rg_electron42.52
Forward intensity I(0) i0323699000.00
Molecular weight molecular_weight144410.0 kDa
Excluded volume excluded_volume179820 ų
Envelope volume envelope_volume237060 ų
Hydration-shell volume shell_volume49567 ų
Envelope diameter envelope_diameter142.7
Shell Rg shell_rg44.55
Envelope Rg envelope_rg41.85
Shape Rg shape_rg42.54
Total Rg total_rg42.55
Total atoms total_atoms10118
Residues n_residues1315
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 dmax143.8
Rg (real space) rg_real42.43
Rg uncertainty (real space) rg_real_error1.35
I(0) (real space) i0_real3.2370e+08
I(0) uncertainty (real space) i0_real_error5.7850e+06
Rg (reciprocal space) rg_reciprocal42.41
I(0) (reciprocal space) i0_reciprocal323700000.0000
Solution quality estimate total_estimate0.8864
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.4
Skewness Skewness skewness0.237
Kurtosis Kurtosis kurtosis-0.606
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha29430000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd4ibxa_
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_idd4ibxb_
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_idd4ibxc_
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_idd4ibxd_
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_idd4ibxe_
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 (5 domains)

Domain ID domain_id4ibxA00
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_id4ibxB00
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_id4ibxC00
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_id4ibxD00
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_id4ibxE00
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)