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- PDB-5fjy: Crystal structure of mouse kinesin light chain 2 (residues 161-480) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fjy | ||||||
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Title | Crystal structure of mouse kinesin light chain 2 (residues 161-480) | ||||||
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![]() | PROTEIN TRANSPORT / MOLECULAR TRANSPORT / TPR DOMAINS / AUTOINHIBITION | ||||||
Function / homology | ![]() 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 / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernigo, S. / Yip, Y.Y. / Sanger, A. / Xu, M. / Dodding, M.P. / Steiner, R.A. | ||||||
![]() | ![]() 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: ![]() Title: Structural Basis for Kinesin-1:Cargo Recognition Authors: Pernigo, S. / Lamprecht, A. / Steiner, R.A. / Dodding, M.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.4 KB | Display | ![]() |
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PDB format | ![]() | 259.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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