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Yorodumi- PDB-3hmo: Crystal structure of human Mps1 catalytic domain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3hmo | ||||||
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Title | Crystal structure of human Mps1 catalytic domain in complex with the inhibitor staurosporine | ||||||
Components | Dual specificity protein kinase TTK | ||||||
Keywords | TRANSFERASE / MPS1 / TTK / STU / STAUROSPORINE / KINASE / ATP-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / spindle / kinetochore / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chu, M.L.H. / Chavas, L.M.G. / Williams, D.H. / Tabernero, L. / Eyers, P.A. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Biophysical and X-ray crystallographic analysis of Mps1 kinase inhibitor complexes. Authors: Chu, M.L. / Lang, Z. / Chavas, L.M. / Neres, J. / Fedorova, O.S. / Tabernero, L. / Cherry, M. / Williams, D.H. / Douglas, K.T. / Eyers, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hmo.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hmo.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/3hmo ftp://data.pdbj.org/pub/pdb/validation_reports/hm/3hmo | HTTPS FTP |
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-Related structure data
Related structure data | 3hmnC 3hmpC 2zmdS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39086.441 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, residues 510-809 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPS1L1, TTK / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LysS / References: UniProt: P33981, dual-specificity kinase |
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-Non-polymers , 5 types, 89 molecules
#2: Chemical | ChemComp-7PE / | ||||
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#3: Chemical | ChemComp-STU / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 % PEG 300, 0.1 M HEPES, 2.5 % Isopropanol, 5 % Glycerol, 50 mM Ammonium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→59.84 Å / Num. obs: 16228 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 47.447 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.101 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 5 / Num. unique all: 10719 / Rsym value: 0.55 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZMD Resolution: 2.4→59.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.168 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.246 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.719 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→59.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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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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