+
Open data
-
Basic information
Entry | Database: PDB / ID: 3odv | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of kaliotoxin by racemic protein crystallography | ||||||
![]() | Potassium channel toxin alpha-KTx 3.1 | ||||||
![]() | TOXIN / Racemic protein / Direct methods / chemical synthesis | ||||||
Function / homology | ![]() ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pentelute, B.L. / Mandal, K. / Gates, Z.P. / Sawaya, M.R. / Yeates, T.O. / Kent, S.B.H. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 4165.052 Da / Num. of mol.: 2 / Fragment: L-Kaliotoxin / Source method: obtained synthetically / Details: Chemical Synthesis Source: (synth.) ![]() References: UniProt: P24662 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.41 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→38.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
|