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Yorodumi- PDB-3hmn: Crystal structure of human Mps1 catalytic domain in complex with ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hmn | ||||||
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Title | Crystal structure of human Mps1 catalytic domain in complex with ATP | ||||||
Components | Dual specificity protein kinase TTK | ||||||
Keywords | TRANSFERASE / MPS1 / TTK / 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 / kinetochore / spindle / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 3hmn.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hmn.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hmn_validation.pdf.gz | 766.1 KB | Display | wwPDB validaton report |
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Full document | 3hmn_full_validation.pdf.gz | 768.3 KB | Display | |
Data in XML | 3hmn_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 3hmn_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/3hmn ftp://data.pdbj.org/pub/pdb/validation_reports/hm/3hmn | HTTPS FTP |
-Related structure data
Related structure data | 3hmoC 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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Unit cell |
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-Components
#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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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-7PE / |
#4: 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: 2.64 Å3/Da / Density % sol: 53.49 % |
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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: 94 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40.36 Å / Num. obs: 11436 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 75.912 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.079 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3 / Num. unique all: 9374 / Rsym value: 0.232 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZMD Resolution: 2.7→40.36 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.141 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.325 / 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: 45.162 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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