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- PDB-6mf5: Crystal structure of budding yeast Cdc5 polo-box domain in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mf5 | ||||||
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Title | Crystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72 phosphopeptide. | ||||||
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![]() | CELL CYCLE / Transferase / Mitosis / Dbf4 / Polo-like kinases | ||||||
Function / homology | ![]() gamma-tubulin complex localization to cytoplasmic side of mitotic spindle pole body / astral microtubule anchoring at mitotic spindle pole body / outer plaque of mitotic spindle pole body / positive regulation of mitotic spindle pole body separation / positive regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / regulation of protein localization to mitotic spindle pole body / Polo-like kinase mediated events / Regulation of PLK1 Activity at G2/M Transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of nucleus organization ...gamma-tubulin complex localization to cytoplasmic side of mitotic spindle pole body / astral microtubule anchoring at mitotic spindle pole body / outer plaque of mitotic spindle pole body / positive regulation of mitotic spindle pole body separation / positive regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / regulation of protein localization to mitotic spindle pole body / Polo-like kinase mediated events / Regulation of PLK1 Activity at G2/M Transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of nucleus organization / mitotic spindle orientation checkpoint signaling / Golgi Cisternae Pericentriolar Stack Reorganization / outer plaque of spindle pole body / negative regulation of protein localization to nucleolus / Resolution of Sister Chromatid Cohesion / meiotic spindle assembly / mitotic spindle astral microtubule end / karyogamy / synaptonemal complex disassembly / astral microtubule organization / polo kinase / centromeric DNA binding / resolution of meiotic recombination intermediates / microtubule nucleation / cellular bud neck / microtubule plus-end binding / spindle pole body / exit from mitosis / microtubule lateral binding / positive regulation of Rho protein signal transduction / cytoplasmic microtubule organization / mitotic spindle organization / phosphoprotein binding / spindle microtubule / kinetochore / spindle pole / protein kinase activity / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guarne, A. / Almawi, A.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division. Authors: Almawi, A.W. / Langlois-Lemay, L. / Boulton, S. / Rodriguez Gonzalez, J. / Melacini, G. / D'Amours, D. / Guarne, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.6 KB | Display | ![]() |
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PDB format | ![]() | 231.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.1 KB | Display | ![]() |
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Full document | ![]() | 462.2 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mf4C ![]() 6mf6C ![]() 1q4oS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33463.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CDC5, MSD2, PKX2, YMR001C, YM8270.03C / Production host: ![]() ![]() #2: Protein/peptide | Mass: 1112.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: synthetic construct (others) / References: UniProt: P39723*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH 6.50, 200 mM magnesium chloride, 100 mM cesium chloride, 25 % PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→42.1 Å / Num. obs: 16158 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.7→2.78 Å / Num. unique obs: 1184 / CC1/2: 0.317 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q4O Resolution: 2.7→42.08 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→42.08 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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