4ibr

Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S/E104K mutations

Method: X-RAY DIFFRACTION Dmax: 58.2 Å Quality: EXCELLENT

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

TEM-94 ES-beta-lactamase

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:A41G, N51A, R119G, M181T, L200A, T262M, G237S, E103K CA CALCIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;11% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES buffer pH 6.7, 200mM Ca(OAc)2 and 10 M ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.247
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–286 Mutation:A41G, N51A, R119G, M181T, L200A, T262M, G237S, E103K CA CALCIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;11% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES buffer pH 6.7, 200mM Ca(OAc)2 and 10 M ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.247

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 154 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

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 4ibr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4ibr
Deposition date deposition_date2012-12-09
Structure title titleCrystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S/E104K mutations
Keywords keywordsbeta-lactamase, 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_electron17.54
Forward intensity I(0) i015275100.00
Molecular weight molecular_weight28995.0 kDa
Excluded volume excluded_volume36144 ų
Envelope volume envelope_volume39731 ų
Hydration-shell volume shell_volume18708 ų
Envelope diameter envelope_diameter58.1
Shell Rg shell_rg24.05
Envelope Rg envelope_rg17.83
Shape Rg shape_rg17.57
Total Rg total_rg18.37
Total atoms total_atoms2030
Residues n_residues263
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 dmax58.2
Rg (real space) rg_real18.67
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real1.5280e+07
I(0) uncertainty (real space) i0_real_error1.8560e+05
Rg (reciprocal space) rg_reciprocal18.69
I(0) (reciprocal space) i0_reciprocal15280000.0000
Solution quality estimate total_estimate0.9010
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.6
Skewness Skewness skewness0.178
Kurtosis Kurtosis kurtosis-0.387
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2915000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.995

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_idd4ibra_
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_id4ibrA00
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)