1jtd

Crystal structure of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase

Method: X-RAY DIFFRACTION Dmax: 78.1 Å Quality: GOOD

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

TEM-1 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–286 Not recorded beta-lactamase inhibitor protein II × 1 (O87916) CA CALCIUM ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;PEG8000, calcium acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.30 Å R-free 0.230

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 155 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLAT_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–263; UniProt 24–286

beta-lactamase inhibitor protein II

OrganismNot specified

UniProt O87916

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 39–311 Not recorded TEM-1 beta-lactamase × 1 (P62593) CA CALCIUM ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;PEG8000, calcium acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.30 Å R-free 0.230

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.

3 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O87916_STREX
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–273; UniProt 39–311

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 1jtd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jtd
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1jtd
Deposition date deposition_date2001-08-20
Structure title titleCrystal structure of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase
Keywords keywordsprotein-protein complex, TEM-1 beta-lactamase, beta-lactamase inhibitor protein-II, BLIP-II, 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_guinier24.44
Radius of gyration Rg (electron density) rg_electron23.65
Forward intensity I(0) i054360700.00
Molecular weight molecular_weight56319.0 kDa
Excluded volume excluded_volume70048 ų
Envelope volume envelope_volume79928 ų
Hydration-shell volume shell_volume27947 ų
Envelope diameter envelope_diameter80.5
Shell Rg shell_rg31.00
Envelope Rg envelope_rg23.71
Shape Rg shape_rg23.62
Total Rg total_rg24.55
Total atoms total_atoms3957
Residues n_residues535
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 dmax78.1
Rg (real space) rg_real24.38
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real5.4360e+07
I(0) uncertainty (real space) i0_real_error7.5320e+05
Rg (reciprocal space) rg_reciprocal24.39
I(0) (reciprocal space) i0_reciprocal54360000.0000
Solution quality estimate total_estimate0.8972
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13380000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1jtda_
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_idd1jtdb_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.5 — RCC1/BLIP-II
Family Family familyb.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

CATH v4.4 (2 domains)

Domain ID domain_id1jtdA00
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_id1jtdB00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

8. Citations (1)

9. Files and Curves (10)