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Yorodumi- PDB-3k5e: The structure of human kinesin-like motor protein Kif11/KSP/Eg5 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k5e | ||||||
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Title | The structure of human kinesin-like motor protein Kif11/KSP/Eg5 in complex with ADP and enastrol. | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | HYDROLASE / motor protein / nucleotide binding. / ATP-binding / Cell cycle / Cell division / Coiled coil / Microtubule / Mitosis / Nucleotide-binding / Phosphoprotein / Polymorphism | ||||||
Function / homology | Function and homology information spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Crawley, L. / Cheng, R.K.Y. / Wood, M. / Barker, J. / Felicetti, B. / Whittaker, M. | ||||||
Citation | Journal: To be Published Title: The structure of human kinesin-like motor protein Kif11/KSP/Eg5 in complex with ADP and enastrol. Authors: Crawley, L. / Cheng, R.K.Y. / Wood, M. / Barker, J. / Felicetti, B. / Whittaker, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k5e.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k5e.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 3k5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k5e ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k5e | HTTPS FTP |
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-Related structure data
Related structure data | 1q0bS S: Starting model for refinement |
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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: 41055.582 Da / Num. of mol.: 2 / Fragment: Motor domain/nucleotide binding, residues 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EG5, KIF11, KNSL1, TRIP5 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P52732, EC: 3.6.4.4 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% PEG3350, 0.1M BisTris pH 6.0, 0.2M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009 Details: Si (111) double crystal monochromator. Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→39.9 Å / Num. obs: 56420 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.34 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q0B Resolution: 1.97→39.9 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.869 / SU B: 5.014 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.181 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→39.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.969→2.02 Å / Total num. of bins used: 20
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