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Yorodumi- PDB-5wwl: Crystal structure of the Schizogenesis pombe kinetochore Mis12C s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wwl | ||||||
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Title | Crystal structure of the Schizogenesis pombe kinetochore Mis12C subcomplex | ||||||
Components |
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Keywords | CELL CYCLE / kinetochore Mis12C | ||||||
Function / homology | Function and homology information MIS12/MIND type complex => GO:0000444 / kinetochore => GO:0000776 / chromosome, centromeric core domain / spindle attachment to meiosis I kinetochore / inner kinetochore / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / mitotic sister chromatid segregation ...MIS12/MIND type complex => GO:0000444 / kinetochore => GO:0000776 / chromosome, centromeric core domain / spindle attachment to meiosis I kinetochore / inner kinetochore / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / mitotic sister chromatid segregation / chromosome segregation / kinetochore / cell division Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Wang, C. / Zhou, X. / Wu, M. / Zhang, X. / Zang, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Phosphorylation of CENP-C by Aurora B facilitates kinetochore attachment error correction in mitosis. Authors: Zhou, X. / Zheng, F. / Wang, C. / Wu, M. / Zhang, X. / Wang, Q. / Yao, X. / Fu, C. / Zhang, X. / Zang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wwl.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wwl.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/5wwl ftp://data.pdbj.org/pub/pdb/validation_reports/ww/5wwl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25232.748 Da / Num. of mol.: 1 / Fragment: UNP residues 1-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: mis12, SPBC409.04c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y738 |
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#2: Protein | Mass: 20310.305 Da / Num. of mol.: 1 / Fragment: UNP residues 1-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: nnf1, SPAC29E6.04, SPAC30.08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09858 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % / Description: cuboid |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 30% (v/v) PEG 400, 0.1M cacodylate pH 6.5, 0.2M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.01 Å / Num. obs: 17989 / % possible obs: 96.3 % / Redundancy: 5 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.3 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.434 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.29 / 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: 51.987 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→50.01 Å
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Refine LS restraints |
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