+Open data
-Basic information
Entry | Database: PDB / ID: 5djo | ||||||
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Title | Crystal structure of the CC1-FHA tandem of Kinesin-3 KIF13A | ||||||
Components | Kinesin-like protein | ||||||
Keywords | TRANSPORT PROTEIN / coiled-coil / FHA domain | ||||||
Function / homology | Function and homology information microtubule motor activity => GO:0003777 / vesicle cargo loading / plus-end-directed vesicle transport along microtubule / Golgi to plasma membrane protein transport / melanosome organization / kinesin complex / microtubule motor activity / endosome to lysosome transport / microtubule-based movement / trans-Golgi network membrane ...microtubule motor activity => GO:0003777 / vesicle cargo loading / plus-end-directed vesicle transport along microtubule / Golgi to plasma membrane protein transport / melanosome organization / kinesin complex / microtubule motor activity / endosome to lysosome transport / microtubule-based movement / trans-Golgi network membrane / regulation of cytokinesis / intracellular protein transport / midbody / microtubule binding / microtubule / endosome membrane / cell cycle / cell division / centrosome / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Ren, J.Q. / Li, W. / Huo, L. / Feng, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A Authors: Ren, J. / Huo, L. / Wang, W. / Zhang, Y. / Li, W. / Lou, J. / Xu, T. / Feng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5djo.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5djo.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 5djo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/5djo ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5djo | HTTPS FTP |
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-Related structure data
Related structure data | 5djnC 3fm8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19807.498 Da / Num. of mol.: 2 / Fragment: UNP residues 386-555 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif13a / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: F8VQ75, UniProt: Q9EQW7*PLUS #2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-ACY / | #4: Chemical | ChemComp-PEG / | #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: 2.09 Å3/Da / Density % sol: 41.25 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: 0.2 M calcium acetate, 16% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→49.55 Å / Num. obs: 33409 / % possible obs: 99 % / Redundancy: 5.1 % / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.74→1.79 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FM8 Resolution: 1.74→40.488 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.77 Å2 / Biso mean: 38.5082 Å2 / Biso min: 14.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→40.488 Å
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Refine LS restraints |
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LS refinement shell |
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