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Yorodumi- PDB-5lt3: nucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lt3 | |||||||||
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Title | nucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form | |||||||||
Components | Kinesin-1 heavy chain | |||||||||
Keywords | MOTOR PROTEIN / Kinesin motor domain / ADP dissociation / nucleotide-free | |||||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / mitochondrion transport along microtubule / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / ciliary rootlet / natural killer cell mediated cytotoxicity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / positive regulation of protein localization to plasma membrane / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / microtubule binding / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | Cao, L. / Gigant, B. | |||||||||
Funding support | France, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: The structural switch of nucleotide-free kinesin. Authors: Cao, L. / Cantos-Fernandes, S. / Gigant, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lt3.cif.gz | 695.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lt3.ent.gz | 575.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lt3_validation.pdf.gz | 497.7 KB | Display | wwPDB validaton report |
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Full document | 5lt3_full_validation.pdf.gz | 522.8 KB | Display | |
Data in XML | 5lt3_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 5lt3_validation.cif.gz | 88.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/5lt3 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/5lt3 | HTTPS FTP |
-Related structure data
Related structure data | 5lt0C 5lt1C 5lt2C 5lt4C 4lnuS 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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Unit cell |
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-Components
#1: Protein | Mass: 36246.719 Da / Num. of mol.: 6 / Mutation: C7S, C65A, T87A, C168A, C174S, C294A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P33176 #2: Chemical | ChemComp-SO4 / #3: 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: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 mM Mes pH 6.5 0.2M ammonium sulfate 30% mPEG 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.9 Å / Num. obs: 59275 / % possible obs: 97.3 % / Redundancy: 2.9 % / CC1/2: 0.967 / Net I/σ(I): 3.8 |
Reflection shell | Highest resolution: 2.59 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LNU Resolution: 2.59→33.176 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.64 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→33.176 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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