+Open data
-Basic information
Entry | Database: PDB / ID: 3odv | ||||||
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Title | X-ray structure of kaliotoxin by racemic protein crystallography | ||||||
Components | Potassium channel toxin alpha-KTx 3.1 | ||||||
Keywords | TOXIN / Racemic protein / Direct methods / chemical synthesis | ||||||
Function / homology | Function and homology information ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Androctonus mauretanicus mauretanicus (scorpion) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å | ||||||
Authors | Pentelute, B.L. / Mandal, K. / Gates, Z.P. / Sawaya, M.R. / Yeates, T.O. / Kent, S.B.H. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2010 Title: Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Authors: Pentelute, B.L. / Mandal, K. / Gates, Z.P. / Sawaya, M.R. / Yeates, T.O. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3odv.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3odv.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 3odv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/3odv ftp://data.pdbj.org/pub/pdb/validation_reports/od/3odv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4165.052 Da / Num. of mol.: 2 / Fragment: L-Kaliotoxin / Source method: obtained synthetically / Details: Chemical Synthesis Source: (synth.) Androctonus mauretanicus mauretanicus (scorpion) References: UniProt: P24662 #2: Chemical | #3: Chemical | #4: 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: 1.74 Å3/Da / Density % sol: 29.41 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.95373 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. all: 62285 / Num. obs: 62285 / % possible obs: 88.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 0.95→0.98 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3600 / % possible all: 50.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.95→38.13 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.469 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R Free: 0.025 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.564 Å2
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Refinement step | Cycle: LAST / Resolution: 0.95→38.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
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