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Yorodumi- PDB-3hh7: Structural and Functional Characterization of a Novel Homodimeric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hh7 | ||||||
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Title | Structural and Functional Characterization of a Novel Homodimeric Three-finger Neurotoxin from the Venom of Ophiophagus hannah (King Cobra) | ||||||
Components | Muscarinic toxin-like protein 3 homolog | ||||||
Keywords | TOXIN / haditoxin / Three finger toxin / Ophiophagus hannah / snake venom / neurotoxin / nicotinic acetylcholine receptors / Acetylcholine receptor inhibitor / Disulfide bond / Postsynaptic neurotoxin / Secreted | ||||||
Function / homology | Function and homology information host cell postsynaptic membrane / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Ophiophagus hannah (king cobra) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Roy, A. / Zhou, X. / Chong, M.Z. / D'hoedt, D. / Foo, C.S. / Rajagopalan, N. / Nirthanan, S. / Bertrand, D. / Sivaraman, J. / Kini, R.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural and Functional Characterization of a Novel Homodimeric Three-finger Neurotoxin from the Venom of Ophiophagus hannah (King Cobra) Authors: Roy, A. / Zhou, X. / Chong, M.Z. / D'hoedt, D. / Foo, C.S. / Rajagopalan, N. / Nirthanan, S. / Bertrand, D. / Sivaraman, J. / 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 | 3hh7.cif.gz | 36.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hh7.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hh7_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 3hh7_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 3hh7_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3hh7_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/3hh7 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hh7 | 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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Unit cell |
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-Components
#1: Protein | Mass: 7552.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ophiophagus hannah (king cobra) / References: UniProt: A8N286 #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 Å3/Da / Density % sol: 38.57 % / Mosaicity: 0.638 ° |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.5 Details: 0.1M Tris, pH 8.5, 20% v/v ethanol, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Mar 3, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. obs: 17366 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Χ2: 7.608 / Net I/σ(I): 40.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.432 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.095 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 37.54 Å2 / Biso mean: 14.997 Å2 / Biso min: 6.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.549→1.589 Å / Total num. of bins used: 20
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