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Yorodumi- PDB-4ary: Lepidopteran-specific toxin Cry1Ac in complex with receptor speci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ary | ||||||
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Title | Lepidopteran-specific toxin Cry1Ac in complex with receptor specificity determinant GalNAc | ||||||
Components | PESTICIDAL CRYSTAL PROTEIN CRY1AC | ||||||
Keywords | TOXIN / MEMBRANE PORE-FORMING TOXIN / INSECTICIDAL PROTEIN / LEPIDOPTERAN SPECIFICITY / CARBOHYDRATE RECOGNITION / MANDUCA SEXTA / AMINOPEPTIDASE N | ||||||
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 SEROVAR KURSTAKI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Derbyshire, D.J. / Carroll, J. / Ellar, D.J. / Li, J. | ||||||
Citation | Journal: To be Published Title: Structural Basis of Galnac-Dependent Receptor Recognition by B. Thuringiensis Toxin Cry1Ac Authors: Derbyshire, D.J. / Carroll, J. / Ellar, D.J. / Li, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization of the Bacillus Thuringiensis Toxin Cry1Ac and its Complex with the Receptor Ligand N-Aceryl-D-Galactosamine Authors: Derbyshire, D.J. / Ellar, D.J. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ary.cif.gz | 448.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ary.ent.gz | 369.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ary.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4ary ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4ary | HTTPS FTP |
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-Related structure data
Related structure data | 4arxSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 0
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 65165.660 Da / Num. of mol.: 4 Fragment: ACTIVATED TOXIN OBTAINED BY TRYPSIN CLEAVAGE, RESIDUES 31-611 Source method: isolated from a natural source Source: (natural) BACILLUS THURINGIENSIS SEROVAR KURSTAKI (bacteria) Variant: HD-73 / References: UniProt: P05068 #2: Sugar | ChemComp-NGA / #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 1,3-DIAMINOPROPANE (13D): USING 1,3-DIAMINOPROPANE AS BUFFER DURING PURIFICATION PREVENTED ...1,3-DIAMINOPRO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | Method: microdialysis / pH: 9.8 Details: MICRODIALYSIS AGAINST 68-70 MM REMARK 280 PIPERAZINE PH 9.8, 28-30 MM NABR, 20-22% GLYCEROL, 9% MPD, 0.5% GALNAC. FOR DETAILS SEE REFERENCE IN REMARK 1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→46.89 Å / Num. obs: 46706 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 59.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CHAIN A OF PDB ENTRY 4ARX Resolution: 2.95→223.61 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.895 / SU B: 19.634 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOCAL NCS RESTRAINTS WERE DEFINED AUTOMATICALLY. JELLY BODY RESTRAINTS AGAINST EXCESSIVE POSITION SHIFTS WERE APPLIED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.961 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→223.61 Å
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Refine LS restraints |
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