← Back to search
1dlc

CRYSTAL STRUCTURE OF INSECTICIDAL DELTA-ENDOTOXIN FROM BACILLUS THURINGIENSIS AT 2.5 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 88.8 Å Quality: GOOD
▼

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

DELTA-ENDOTOXIN CRYIIIA

Bacillus thuringiensis

UniProt P0A379

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 61–644 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å

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.

Other PDB Difference from Current Entry 1DLC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4QX0 Cry3A Toxin structure obtained by Serial Femtosecond Crystallography from in vivo grown crystals isolated from Bacillus thuringiensis and data processed with the cctbx.xfel software suite Deposited 2014-07-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 58–644（587 aa） Fragment：UNP residues 58-644
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions IN VIVO CRYSTALLIZATION；303 K；Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K
Resolution 2.80 Å R-free 0.192
4QX1 Cry3A Toxin structure obtained by Serial Femtosecond Crystallography from in vivo grown crystals isolated from Bacillus thuringiensis and data processed with the CrystFEL software suite Deposited 2014-07-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 58–644（587 aa） Fragment：UNP residues 58-644
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions IN VIVO CRYSTALLIZATION；303 K；Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K
Resolution 2.80 Å R-free 0.197
4QX2 Cry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the cctbx.xfel software suite Deposited 2014-07-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 58–644（587 aa） Fragment：UNP residues 58-644
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions IN VIVO CRYSTALLIZATION；303 K；Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K
Resolution 2.90 Å R-free 0.201
4QX3 Cry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the CrystFEL software suite Deposited 2014-07-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 58–644（587 aa） Fragment：UNP residues 58-644
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions IN VIVO CRYSTALLIZATION；303 K；Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K
Resolution 2.90 Å R-free 0.194

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CR3AA_BACTT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–584； UniProt 61–644

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 1dlc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dlc
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1dlc
Deposition date deposition_date1994-06-22
Structure title titleCRYSTAL STRUCTURE OF INSECTICIDAL DELTA-ENDOTOXIN FROM BACILLUS THURINGIENSIS AT 2.5 ANGSTROMS RESOLUTION
Keywords keywordsTOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier26.75 Å
Radius of gyration Rg (electron density) rg_electron25.56 Å
Forward intensity I(0) i069821300.00
Molecular weight molecular_weight66241.0 kDa
Excluded volume excluded_volume83080 ų
Envelope volume envelope_volume97729 ų
Hydration-shell volume shell_volume31831 ų
Envelope diameter envelope_diameter93.4 Å
Shell Rg shell_rg32.92 Å
Envelope Rg envelope_rg25.76 Å
Shape Rg shape_rg25.57 Å
Total Rg total_rg26.29 Å
Total atoms total_atoms4690
Residues n_residues584
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax88.8 Å
Rg (real space) rg_real26.68 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real6.9820e+07
I(0) uncertainty (real space) i0_real_error1.0610e+06
Rg (reciprocal space) rg_reciprocal26.70 Å
I(0) (reciprocal space) i0_reciprocal69820000.0000
Solution quality estimate total_estimate0.8822
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.6 Å
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.294
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15750000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.917
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1dlca1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.3 — delta-Endotoxin, C-terminal domain
Domain ID domain_idd1dlca2
Class classb — All beta proteins
Fold Fold foldb.77 — beta-Prism I
Superfamily Superfamily superfamilyb.77.2 — delta-Endotoxin (insectocide), middle domain
Family Family familyb.77.2.1 — delta-Endotoxin (insectocide), middle domain
Domain ID domain_idd1dlca3
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamilyf.1.3 — delta-Endotoxin (insectocide), N-terminal domain
Family Family familyf.1.3.1 — delta-Endotoxin (insectocide), N-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id1dlcA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily10 — Pesticidal crystal protein, N-terminal domain
Domain ID domain_id1dlcA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id1dlcA03
Class class2 — Mainly Beta
Architecture architecture100 — Aligned Prism
Topology topology10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily10 — Pesticidal crystal protein, central domain
▶

8. Citations (2)

▶

9. Files and Curves (10)