+Open data
-Basic information
Entry | Database: PDB / ID: 3hqd | ||||||
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Title | Human kinesin Eg5 motor domain in complex with AMPPNP and Mg2+ | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | MOTOR PROTEIN / kinesin / motor domain / ATP hydrolysis / mitosis / spindle protein / ATP-binding / Cell cycle / Cell division / Coiled coil / Microtubule / 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 / spindle / spindle pole / mitotic spindle / 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 / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Parke, C.L. / Wojcik, E.J. / Kim, S. / Worthylake, D.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: ATP Hydrolysis in Eg5 Kinesin Involves a Catalytic Two-water Mechanism. Authors: Parke, C.L. / Wojcik, E.J. / Kim, S. / Worthylake, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hqd.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hqd.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/3hqd ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqd | HTTPS FTP |
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-Related structure data
Related structure data | 1x88S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41168.738 Da / Num. of mol.: 2 Fragment: motor domain of human kinesin Eg5 (residues 1-369) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EG5, KIF11, KNSL1, TRIP5 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P52732 #2: Chemical | #3: Chemical | ChemComp-PO4 / | #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: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 40 mM KH2PO4, 20% glycerol w/v, 15% PEG 8k w/v, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→28.69 Å / Num. all: 41542 / Num. obs: 41542 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.85 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.1188 / Rsym value: 0.089 / Net I/σ(I): 9.35 |
Reflection shell | Resolution: 2.19→2.29 Å / Redundancy: 1.89 % / Rmerge(I) obs: 0.5481 / Mean I/σ(I) obs: 2.27 / Rsym value: 0.335 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1X88 molecule A Resolution: 2.19→25 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 38.559 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.859 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→25 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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