+Open data
-Basic information
Entry | Database: PDB / ID: 6a20 | ||||||
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Title | Crystal Structure of auto-inhibited Kinesin-3 KIF13B | ||||||
Components | Kinesin family member 13BKinesin-like protein KIF13B | ||||||
Keywords | TRANSPORT PROTEIN / kinesin / ATPase | ||||||
Function / homology | Function and homology information Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / paranode region of axon / kinesin complex / microtubule motor activity / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding ...Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / paranode region of axon / kinesin complex / microtubule motor activity / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding / microtubule binding / microtubule / axon / protein kinase binding / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ren, J.Q. / Wang, S. / Feng, W. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Coiled-coil 1-mediated fastening of the neck and motor domains for kinesin-3 autoinhibition. Authors: Ren, J.Q. / Wang, S. / Chen, H. / Wang, W.J. / Huo, L. / Feng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a20.cif.gz | 178 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a20.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 6a20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/6a20 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/6a20 | HTTPS FTP |
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-Related structure data
Related structure data | 6a1zC 5zbsS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 48970.270 Da / Num. of mol.: 1 / Mutation: Y73C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kif13b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2K8Z9 | ||||
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#2: Chemical | ChemComp-ADP / | ||||
#3: Chemical | #4: Chemical | ChemComp-P6G / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.31 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7.5 Details: 0.2M proline, 0.1M HEPES, pH 7.5, 14% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 22223 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.615 / Num. unique obs: 3271 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZBS Resolution: 2.4→30.639 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30.639 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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