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Yorodumi- PDB-5fjy: Crystal structure of mouse kinesin light chain 2 (residues 161-480) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fjy | ||||||
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Title | Crystal structure of mouse kinesin light chain 2 (residues 161-480) | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / MOLECULAR TRANSPORT / TPR DOMAINS / AUTOINHIBITION | ||||||
Function / homology | Function and homology information RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / lysosome localization / MHC class II antigen presentation / axo-dendritic transport / ciliary rootlet / kinesin complex / microtubule-based movement / kinesin binding ...RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / lysosome localization / MHC class II antigen presentation / axo-dendritic transport / ciliary rootlet / kinesin complex / microtubule-based movement / kinesin binding / microtubule / neuron projection / lysosomal membrane / protein-containing complex / mitochondrion / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Pernigo, S. / Yip, Y.Y. / Sanger, A. / Xu, M. / Dodding, M.P. / Steiner, R.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: The Light Chains of Kinesin-1 are Autoinhibited. Authors: Yip, Y.Y. / Pernigo, S. / Sanger, A. / Xu, M. / Parsons, M. / Steiner, R.A. / Dodding, M.P. #1: Journal: Science / Year: 2013 Title: Structural Basis for Kinesin-1:Cargo Recognition Authors: Pernigo, S. / Lamprecht, A. / Steiner, R.A. / Dodding, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjy.cif.gz | 311.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjy.ent.gz | 259.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjy ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36370.984 Da / Num. of mol.: 3 / Fragment: TPR DOMAIN WITH N-TERMINAL EXTENSION Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91YS4, UniProt: O88448*PLUS #2: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: PEPTIDE MAY BE PART OF TPR N-TERMINAL EXTENSION / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) Nonpolymer details | UNKNOWN AMINO ACID (UNK): RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL ...UNKNOWN AMINO ACID (UNK): RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL EXTENSION. DUE TO THE LOW RESOLUTION | Sequence details | THE FIRST FOUR AMINO ACIDS DERIVE FROM THE CLONING STRATEGY | |
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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: 3.25 Å3/Da / Density % sol: 62.15 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 8% (W/V) PGA-LM 0.3 M NA-MALONATE 0.1 M NA-CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 4→42.88 Å / Num. obs: 11813 / % possible obs: 98.4 % / Observed criterion σ(I): -1 / Redundancy: 3 % / Biso Wilson estimate: 163 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 4→4.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 0.6 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3CEQ AND 3ZFW Resolution: 4→42.88 Å / Cor.coef. Fo:Fc: 0.9119 / Cor.coef. Fo:Fc free: 0.9143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.745 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL EXTENSION. DUE TO THE LOW RESOLUTION ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL EXTENSION. DUE TO THE LOW RESOLUTION OF THE DATA WE ARE UNABLE TO DEFINE THEIR CORRECT IDENTITY.
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Displacement parameters | Biso mean: 266.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.799 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→42.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.38 Å / Total num. of bins used: 6
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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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