+Open data
-Basic information
Entry | Database: PDB / ID: 6mje | ||||||
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Title | Structure of Candida glabrata Csm1: S. cerevisiae Dsn1 complex | ||||||
Components |
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Keywords | CELL CYCLE / monopolin / kinetochore | ||||||
Function / homology | Function and homology information MIS12/MIND type complex / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / attachment of spindle microtubules to kinetochore / mitotic sister chromatid segregation / Neutrophil degranulation / chromosome segregation ...MIS12/MIND type complex / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / attachment of spindle microtubules to kinetochore / mitotic sister chromatid segregation / Neutrophil degranulation / chromosome segregation / kinetochore / spindle pole / nuclear envelope / cell division / nucleolus / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Singh, N. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chromosoma / Year: 2019 Title: The molecular basis of monopolin recruitment to the kinetochore. Authors: Plowman, R. / Singh, N. / Tromer, E.C. / Payan, A. / Duro, E. / Spanos, C. / Rappsilber, J. / Snel, B. / Kops, G.J.P.L. / Corbett, K.D. / Marston, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mje.cif.gz | 240.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mje.ent.gz | 193.4 KB | Display | PDB format |
PDBx/mmJSON format | 6mje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/6mje ftp://data.pdbj.org/pub/pdb/validation_reports/mj/6mje | HTTPS FTP |
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-Related structure data
Related structure data | 6mj8C 6mjbC 6mjcC 3n4rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/610 / Data set type: diffraction image data / Details: SBGrid |
-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
#1: Protein | Mass: 15571.603 Da / Num. of mol.: 4 / Fragment: UNP residues 69-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (fungus) / Gene: AO440_000897, AO440_004693 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0CH22, UniProt: Q6FVN3*PLUS #2: Protein/peptide | Mass: 4763.462 Da / Num. of mol.: 4 / Fragment: UNP residues 71-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DSN1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4A9Z4, UniProt: P40568*PLUS |
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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: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25% PEG3350, cryoprotect with additional 20% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.127 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 26122 / % possible obs: 96 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.091 / Rrim(I) all: 0.219 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.793 / Num. unique obs: 1446 / Rpim(I) all: 0.488 / Rrim(I) all: 0.938 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3N4R Resolution: 2.5→43.351 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 43.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.351 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.1476 Å / Origin y: -24.6765 Å / Origin z: 4.351 Å
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Refinement TLS group | Selection details: all |