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- PDB-5u1t: Crystal structure of the Saccharomyces cerevisiae separase-securi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u1t | |||||||||
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Title | Crystal structure of the Saccharomyces cerevisiae separase-securin complex at 2.6 angstrom resolution | |||||||||
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![]() | HYDROLASE / separase-securin complex / ESP1 / PDS1 / chromosome segregation / cohesion / helical region / inhibition / chaperon | |||||||||
Function / homology | ![]() 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 / negative regulation of phosphoprotein phosphatase activity / mitotic sister chromatid segregation / molecular function activator activity / protein localization / mitotic spindle / spindle / cell division / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / enzyme binding / mitochondrion / proteolysis / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Luo, S. / Tong, L. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.1 KB | Display | ![]() |
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PDB format | ![]() | 257.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 485.1 KB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 74.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u1sSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 184044.469 Da / Num. of mol.: 1 Fragment: UNP residues 71-1630, helical domain and catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: ESP1, YGR098C / Plasmid: pFL / Production host: ![]() |
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: PDS1, YDR113C, YD9727.08C / Plasmid: pFL / Production host: ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2016 / Details: DECTRIS PILATUS 6M-F | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 77491 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 62.34 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.059 / Rrim(I) all: 0.153 / Χ2: 1.06 / Net I/av σ(I): 14.42 / Net I/σ(I): 4.3 / Num. measured all: 774372 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U1S Resolution: 2.6→48.667 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.36 Å2 / Biso mean: 72.031 Å2 / Biso min: 35.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.667 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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