+Open data
-Basic information
Entry | Database: PDB / ID: 1pp6 | ||||||
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Title | VVA2 (STRIP CRYSTAL FORM) | ||||||
Components | Volvatoxin A2 | ||||||
Keywords | TOXIN / Volvatoxin A2 / strip crystal form | ||||||
Function / homology | Delta-endotoxin CytB / Delta-endotoxin CytB-like / Delta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / extracellular region / 3-Layer(aba) Sandwich / Alpha Beta / Volvatoxin A2 Function and homology information | ||||||
Biological species | Volvariella volvacea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Lin, S.-C. / Lo, Y.-C. / Lin, J.-Y. / Liaw, Y.-C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structures and electron micrographs of fungal volvatoxin A2 Authors: Lin, S.-C. / Lo, Y.-C. / Lin, J.-Y. / Liaw, Y.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pp6.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pp6.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1pp6 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1pp6 | HTTPS FTP |
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-Related structure data
Related structure data | 1pp0SC 1vcyC 1vgfC 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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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 22356.961 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Volvariella volvacea (fungus) / References: UniProt: Q6USC4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate, PEG 8000, glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1.0446 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0446 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→28.54 Å / Num. all: 20087 / Num. obs: 19692 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.2→3.24 Å / Rmerge(I) obs: 0.472 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PP0 Resolution: 3.2→28.54 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 35.69 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.68 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→28.54 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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