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Yorodumi- PDB-5u1s: Crystal structure of the Saccharomyces cerevisiae separase-securi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u1s | |||||||||
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Title | Crystal structure of the Saccharomyces cerevisiae separase-securin complex at 3.0 angstrom resolution | |||||||||
Components |
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Keywords | HYDROLASE / separase-securin complex / ESP1 / PDS1 / chromosome segregation / cohesion / helical region / inhibition / chaperon | |||||||||
Function / homology | Function and homology information positive regulation of metaphase/anaphase transition of meiotic cell cycle / Separation of Sister Chromatids / separase-securin complex / separase / negative regulation of protein localization to nucleolus / negative regulation of exit from mitosis / regulation of mitotic spindle elongation / meiotic chromosome separation / positive regulation of exit from mitosis / mitotic spindle pole body ...positive regulation of metaphase/anaphase transition of meiotic cell cycle / Separation of Sister Chromatids / separase-securin complex / separase / negative regulation of protein localization to nucleolus / negative regulation of exit from mitosis / regulation of mitotic spindle elongation / meiotic chromosome separation / positive regulation of exit from mitosis / mitotic spindle pole body / : / meiosis I / recombinational repair / mitotic sister chromatid segregation / molecular function activator activity / mitotic spindle / spindle / protein localization / cell division / cysteine-type endopeptidase activity / DNA damage response / apoptotic process / enzyme binding / mitochondrion / proteolysis / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.002 Å | |||||||||
Authors | Luo, S. / Tong, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2017 Title: Molecular mechanism for the regulation of yeast separase by securin. Authors: Luo, S. / Tong, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u1s.cif.gz | 649.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u1s.ent.gz | 536 KB | Display | PDB format |
PDBx/mmJSON format | 5u1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u1s_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 5u1s_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 5u1s_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 5u1s_validation.cif.gz | 68.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/5u1s ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u1s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 184044.469 Da / Num. of mol.: 1 Fragment: UNP residues 51-1630, helical domain and catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ESP1, YGR098C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five Cell / References: UniProt: Q03018, separase |
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#2: Protein | Mass: 13366.599 Da / Num. of mol.: 1 Fragment: UNP residues 258-373, separase interaction segment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: PDS1, YDR113C, YD9727.08C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five Cell / References: UniProt: P40316 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.49 % / Mosaicity: 0.573 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 0.25 M Na/K-phosphate (pH 6.0) and 14% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2016 / Details: LR-Design detector positioner | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 51156 / % possible obs: 99.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 86.6 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Χ2: 1.032 / Net I/σ(I): 6.3 / Num. measured all: 533070 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 3.002→48.975 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 246.55 Å2 / Biso mean: 96.4093 Å2 / Biso min: 40.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.002→48.975 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Origin x: -80.5655 Å / Origin y: 18.0194 Å / Origin z: 24.4849 Å
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Refinement TLS group |
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