+Open data
-Basic information
Entry | Database: PDB / ID: 2dda | ||||||
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Title | Crystal structure of pseudechetoxin from Pseudechis australis | ||||||
Components | Pseudechetoxin | ||||||
Keywords | TOXIN / CRISP / snake venom / CNG channel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudechis australis (mulga snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Suzuki, N. / Yamazaki, Y. / Fujimoto, Z. / Morita, T. / Mizuno, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain Authors: Suzuki, N. / Yamazaki, Y. / Brown, R.L. / Fujimoto, Z. / Morita, T. / Mizuno, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dda.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dda.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dda_validation.pdf.gz | 468.9 KB | Display | wwPDB validaton report |
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Full document | 2dda_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 2dda_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 2dda_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/2dda ftp://data.pdbj.org/pub/pdb/validation_reports/dd/2dda | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 23761.627 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudechis australis (mulga snake) / Tissue: venom / References: UniProt: Q8AVA4 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-GOL / | #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: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.4M sodium formate, 6.7%(w/v) glycerol, 0.15M NaCl, 50mM Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2004 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 42215 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3.5 / % possible all: 72.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.946 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.248 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.282 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→48.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.251→2.31 Å / Total num. of bins used: 20
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