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- PDB-4ary: Lepidopteran-specific toxin Cry1Ac in complex with receptor speci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ary | ||||||
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Title | Lepidopteran-specific toxin Cry1Ac in complex with receptor specificity determinant GalNAc | ||||||
![]() | PESTICIDAL CRYSTAL PROTEIN CRY1AC | ||||||
![]() | TOXIN / MEMBRANE PORE-FORMING TOXIN / INSECTICIDAL PROTEIN / LEPIDOPTERAN SPECIFICITY / CARBOHYDRATE RECOGNITION / MANDUCA SEXTA / AMINOPEPTIDASE N | ||||||
Function / homology | ![]() symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Derbyshire, D.J. / Carroll, J. / Ellar, D.J. / Li, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 448.7 KB | Display | ![]() |
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PDB format | ![]() | 369.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.5 KB | Display | ![]() |
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Full document | ![]() | 493.1 KB | Display | |
Data in XML | ![]() | 73.7 KB | Display | |
Data in CIF | ![]() | 101.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4arxSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _
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) ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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