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Yorodumi- PDB-6oec: Yeast Spc42 Trimeric Coiled-Coil Amino Acids 181-211 fused to PDB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oec | ||||||
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Title | Yeast Spc42 Trimeric Coiled-Coil Amino Acids 181-211 fused to PDB: 3H5I | ||||||
Components | Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42 | ||||||
Keywords | STRUCTURAL PROTEIN / Yeast Centrosome / Spindle Pole Body / Trimeric Coiled-coil | ||||||
Function / homology | Function and homology information intermediate layer of spindle pole body / central plaque of spindle pole body / spindle pole body duplication / regulation of microtubule nucleation / phosphorelay signal transduction system / structural constituent of cytoskeleton / DNA repair / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Carboxydothermus hydrogenoformans (bacteria) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.514 Å | ||||||
Authors | Drennan, A.C. / Shivaani, K. / Seeger, M.A. / Andreas, M.P. / Gardner, J.M. / Sether, E.K.R. / Jasperson, S.L. / Rayment, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol.Biol.Cell / Year: 2019 Title: Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication. Authors: Drennan, A.C. / Krishna, S. / Seeger, M.A. / Andreas, M.P. / Gardner, J.M. / Sether, E.K.R. / Jaspersen, S.L. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oec.cif.gz | 357.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oec.ent.gz | 292.9 KB | Display | PDB format |
PDBx/mmJSON format | 6oec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oec_validation.pdf.gz | 533.8 KB | Display | wwPDB validaton report |
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Full document | 6oec_full_validation.pdf.gz | 562.6 KB | Display | |
Data in XML | 6oec_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 6oec_validation.cif.gz | 83.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/6oec ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oec | HTTPS FTP |
-Related structure data
Related structure data | 6od2C 6oeiC 3h5iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 17812.424 Da / Num. of mol.: 12 / Mutation: T193E, S195E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC BAA-161 / DSM 6008 / Z-2901, ATCC 204508 / S288c Gene: CHY_0880, SPC42, YKL042W, YKL255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ADQ4, UniProt: P36094 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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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: 3.22 Å3/Da / Density % sol: 61.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Crystals grown from 1:1 mixture of 12 mg/ml protein stored in 20 mM HEPES pH 7.6, 100 mM NaCl and a well solution consiting of 100 mM PIPES pH 6.0, 10% (w/v) MEPEG 5K, 700 mM tetramethylamine chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97962 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 13, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97962 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 88519 / % possible obs: 94.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.034 / Rrim(I) all: 0.101 / Χ2: 0.744 / Net I/σ(I): 5.3 / Num. measured all: 527628 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H5I Resolution: 2.514→48.142 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 23.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.28 Å2 / Biso mean: 45.9306 Å2 / Biso min: 10.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.514→48.142 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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