+Open data
-Basic information
Entry | Database: PDB / ID: 6a1z | ||||||
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Title | Crystal Structure of dimeric 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: 2.58 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 | 6a1z.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a1z.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/6a1z ftp://data.pdbj.org/pub/pdb/validation_reports/a1/6a1z | HTTPS FTP |
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-Related structure data
Related structure data | 6a20C 5zbrS 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: 43923.594 Da / Num. of mol.: 1 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: 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: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 6.9 / Details: 1.4M Na/KPO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→39.87 Å / Num. obs: 13889 / % possible obs: 99.4 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.58→2.65 Å / Rmerge(I) obs: 0.665 / Num. unique obs: 1023 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZBR Resolution: 2.58→39.869 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→39.869 Å
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Refine LS restraints |
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LS refinement shell |
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