+Open data
-Basic information
Entry | Database: PDB / ID: 3uto | ||||||
---|---|---|---|---|---|---|---|
Title | Twitchin kinase region from C.elegans (Fn31-NL-kin-CRD-Ig26) | ||||||
Components | Twitchin | ||||||
Keywords | TRANSFERASE / kinase / muscle sarcomere | ||||||
Function / homology | Function and homology information : / positive regulation of locomotion / Platelet degranulation / positive regulation of sarcomere organization / positive regulation of striated muscle contraction / negative regulation of cell division / behavioral response to nicotine / A band / adult locomotory behavior / calmodulin binding ...: / positive regulation of locomotion / Platelet degranulation / positive regulation of sarcomere organization / positive regulation of striated muscle contraction / negative regulation of cell division / behavioral response to nicotine / A band / adult locomotory behavior / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Castelmur, E. / Barbieri, S. / Mayans, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Identification of an N-terminal inhibitory extension as the primary mechanosensory regulator of twitchin kinase. Authors: von Castelmur, E. / Strumpfer, J. / Franke, B. / Bogomolovas, J. / Barbieri, S. / Qadota, H. / Konarev, P.V. / Svergun, D.I. / Labeit, S. / Benian, G.M. / Schulten, K. / Mayans, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3uto.cif.gz | 455.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3uto.ent.gz | 374.5 KB | Display | PDB format |
PDBx/mmJSON format | 3uto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/3uto ftp://data.pdbj.org/pub/pdb/validation_reports/ut/3uto | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 65245.203 Da / Num. of mol.: 2 Fragment: twitchin kinase region (Fn3-NL-kin-CRD-Ig), UNP residues 6108-6675 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-22, ZK617.1 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) References: UniProt: Q23551, non-specific serine/threonine protein kinase |
---|
-Non-polymers , 5 types, 428 molecules
#2: Chemical | ChemComp-GOL / |
---|---|
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-FLC / |
#5: Chemical | ChemComp-P33 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 600, 100 mM sodium citrate pH 5.5, 50 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.87 Å / Num. obs: 45313 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 4.86 % / Rsym value: 0.097 / Net I/σ(I): 14.43 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 4.82 % / Num. unique all: 2670 / Rsym value: 0.58 / % possible all: 96.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.84 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.242 / 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: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.693 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.87 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|