+Open data
-Basic information
Entry | Database: PDB / ID: 8yhh | ||||||
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Title | The Crystal Structure of Mitotic Kinesin Eg5 from Biortus | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | CELL CYCLE / Motor protein / Cell division / ATP-binding | ||||||
Function / homology | Function and homology information spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle microtubule / mitotic spindle / spindle pole / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of Mitotic Kinesin Eg5 from Biortus Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yhh.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yhh.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 8yhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yhh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8yhh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8yhh_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 8yhh_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/8yhh ftp://data.pdbj.org/pub/pdb/validation_reports/yh/8yhh | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 17 - 364 / Label seq-ID: 19 - 366
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41169.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52732 |
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-Non-polymers , 7 types, 347 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-NO3 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 19% PEG3350, 0.1M MES (pH 5.2), and 200 mM NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.59 Å / Num. obs: 51970 / % possible obs: 96.1 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 3726 / CC1/2: 0.806 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.671 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.174 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→46.59 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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