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Yorodumi- PDB-1onj: Crystal structure of Atratoxin-b from Chinese cobra venom of Naja atra -
+Open data
-Basic information
Entry | Database: PDB / ID: 1onj | ||||||
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Title | Crystal structure of Atratoxin-b from Chinese cobra venom of Naja atra | ||||||
Components | Cobrotoxin b | ||||||
Keywords | TOXIN / beta-turn-beta / three-finger protein | ||||||
Function / homology | Function and homology information acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Naja atra (Chinese cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.555 Å | ||||||
Authors | Lou, X. / Tu, X. / Pan, G. / Xu, C. / Fan, R. / Lu, W. / Deng, W. / Rao, P. / Teng, M. / Niu, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Purification, N-terminal sequencing, crystallization and preliminary structural determination of atratoxin-b, a short-chain alpha-neurotoxin from Naja atra venom. Authors: Lou, X. / Tu, X. / Pan, G. / Xu, C. / Fan, R. / Lu, W. / Deng, W. / Rao, P. / Teng, M. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1onj.cif.gz | 21 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1onj.ent.gz | 16.2 KB | Display | PDB format |
PDBx/mmJSON format | 1onj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1onj_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 1onj_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 1onj_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1onj_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1onj ftp://data.pdbj.org/pub/pdb/validation_reports/on/1onj | 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: 6843.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: P80958 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.62 Å3/Da / Density % sol: 23.42 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.5 Details: ammonium sulfate, Tris-HCl, pH 8.5, EVAPORATION, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRL / Beamline: U7B / Wavelength: 1.1516 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2002 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1516 Å / Relative weight: 1 |
Reflection | Resolution: 1.555→16.57 Å / Num. obs: 8222 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.56→1.64 Å / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.56 Å / Num. obs: 8305 / Num. measured all: 87491 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.555→16.507 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.555→16.507 Å
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Refinement | *PLUS Highest resolution: 1.56 Å / Lowest resolution: 16.57 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |