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Yorodumi- PDB-1dlc: CRYSTAL STRUCTURE OF INSECTICIDAL DELTA-ENDOTOXIN FROM BACILLUS T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dlc | ||||||
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Title | CRYSTAL STRUCTURE OF INSECTICIDAL DELTA-ENDOTOXIN FROM BACILLUS THURINGIENSIS AT 2.5 ANGSTROMS RESOLUTION | ||||||
Components | DELTA-ENDOTOXIN CRYIIIA | ||||||
Keywords | TOXIN | ||||||
Function / homology | Function and homology information symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Li, J. | ||||||
Citation | Journal: Nature / Year: 1991 Title: Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 A resolution. Authors: Li, J.D. / Carroll, J. / Ellar, D.J. #1: Journal: J.Mol.Biol. / Year: 1988 Title: X-Ray Analysis of the Crystalline Parasporal Inclusion in Bacillus Thuringiensis Var. Tenebrionis Authors: Li, J. / Henderson, R. / Carroll, J. / Ellar, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dlc.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dlc.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dlc ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dlc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE ARG 443 IS MODELED IN TWO CONFORMATIONS. |
-Components
#1: Protein | Mass: 66312.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / References: UniProt: P0A379 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF CRYIIIA IN THE ATOMIC MODEL IS TAKEN FROM: HOEFTE, H., SEURINCK, J., VAN HOUTVEN, A. ...THE SEQUENCE OF CRYIIIA IN THE ATOMIC MODEL IS TAKEN FROM: HOEFTE, H., SEURINCK, J., VAN HOUTVEN, A. AND VAECK, M. (1987) NUCLEIC ACIDS RES. 15:7183. EMBL ACCESSION NUMBER P07130, ENTRY NAME CR70_BACTT. RESIDUES 1 - 57 ARE REMOVED IN THE MATURE TOXIN. RESIDUES 58 - 60 ARE INVISIBLE IN THE CRYSTAL STRUCTURE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.26 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 9.5 / Method: microdialysis | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 27727 / Num. measured all: 121767 / Rmerge(I) obs: 0.108 |
-Processing
Software |
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Refinement | Resolution: 2.5→16 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.5→16 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.58 |