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Yorodumi- PDB-2h5f: Denmotoxin: A the three-finger toxin from colubrid snake Boiga de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h5f | ||||||
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Title | Denmotoxin: A the three-finger toxin from colubrid snake Boiga dendrophila with bird-specific activity | ||||||
Components | denmotoxin | ||||||
Keywords | TOXIN / three-finger toxin / neurotoxin / snake venom | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Boiga dendrophila (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Pawlak, J. / Kini, R.M. / Stura, E.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Denmotoxin, a three-finger toxin from the colubrid snake Boiga dendrophila (Mangrove Catsnake) with bird-specific activity. Authors: Pawlak, J. / Mackessy, S.P. / Fry, B.G. / Bhatia, M. / Mourier, G. / Fruchart-Gaillard, C. / Servent, D. / Menez, R. / Stura, E. / Menez, A. / Kini, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h5f.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h5f.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 2h5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h5f_validation.pdf.gz | 452.7 KB | Display | wwPDB validaton report |
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Full document | 2h5f_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 2h5f_validation.xml.gz | 13 KB | Display | |
Data in CIF | 2h5f_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/2h5f ftp://data.pdbj.org/pub/pdb/validation_reports/h5/2h5f | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8547.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Boiga dendrophila (snake) / Secretion: venom / References: UniProt: P83490, UniProt: Q06ZW0*PLUS #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 1.2M Na, KPO4, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.006768 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006768 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→52 Å / Num. obs: 50240 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.74 Å / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.221 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.878 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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