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Yorodumi- PDB-5t59: Structure of the MIND Complex Shows a Regulatory Focus of Yeast K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t59 | ||||||
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Title | Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly | ||||||
Components |
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Keywords | CELL CYCLE / kinetochore / complex / chromosome / segregation / MIND / Mis12 | ||||||
Function / homology | Function and homology information MIS12/MIND type complex / centromeric DNA binding / kinetochore assembly / mitotic spindle organization / chromosome segregation / kinetochore / mitotic cell cycle / cell division / protein-containing complex binding / nucleus Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.405 Å | ||||||
Authors | Dimitrova, Y. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C. | ||||||
Citation | Journal: Cell / Year: 2016 Title: Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly. Authors: Dimitrova, Y.N. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t59.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t59.ent.gz | 154.7 KB | Display | PDB format |
PDBx/mmJSON format | 5t59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/5t59 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/5t59 | HTTPS FTP |
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-Related 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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Details | Trimer confirmed by gel filtration |
-Components
#1: Protein | Mass: 13870.916 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues Asn0 and Ala1 are left over from the TEV cleavage site. Mtw1 starts at residue Thr2. Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_F02343g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CLK3 #2: Protein | Mass: 12100.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_E05809g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPD1 #3: Protein/peptide | Mass: 4826.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_B13629g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CVA1 #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: 54.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES, pH 9.0, 18-30 % PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.405→66.17 Å / Num. obs: 16798 / % possible obs: 56.5 % / Redundancy: 3.6 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.405→66.168 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.39
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.405→66.168 Å
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Refine LS restraints |
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LS refinement shell |
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