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Open data
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Basic information
Entry | Database: PDB / ID: 2ddb | ||||||
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Title | Crystal structure of pseudecin from Pseudechis porphyriacus | ||||||
![]() | Pseudecin | ||||||
![]() | TOXIN / CRISP / snake venom / CNG channel | ||||||
Function / homology | ![]() ion channel regulator activity / toxin activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, N. / Yamazaki, Y. / Fujimoto, Z. / Morita, T. / Mizuno, H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.7 KB | Display | ![]() |
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PDB format | ![]() | 153.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.3 KB | Display | ![]() |
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Full document | ![]() | 489.1 KB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 58.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ddaC ![]() 2epfC ![]() 1wvrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23622.299 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) ![]() Tissue: venom / References: UniProt: Q8AVA3 #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 3.6M sodium formate, 10%(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: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 74335 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7454 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WVR Resolution: 1.9→43.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.842 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.161 / 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 mean: 26.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→43.27 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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