+Open data
-Basic information
Entry | Database: PDB / ID: 8qry | ||||||
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Title | Crystal structure of the yeast spindle body component Spc98 | ||||||
Components | Spindle pole body component | ||||||
Keywords | CELL CYCLE / yeast cell division / yeast spindle pole body | ||||||
Function / homology | Function and homology information mitotic spindle pole body / equatorial microtubule organizing center / microtubule minus-end binding / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole ...mitotic spindle pole body / equatorial microtubule organizing center / microtubule minus-end binding / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Bellini, D. / Yatskevich, S. / Barford, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the yeast spindle body component Spc98 Authors: Bellini, D. / Yatskevich, S. / Barford, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qry.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qry.ent.gz | 20.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qry_validation.pdf.gz | 416.1 KB | Display | wwPDB validaton report |
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Full document | 8qry_full_validation.pdf.gz | 418 KB | Display | |
Data in XML | 8qry_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 8qry_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/8qry ftp://data.pdbj.org/pub/pdb/validation_reports/qr/8qry | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10826.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPC98 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8H4BVY6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Morpheus B4: PEG 3350/PEG 1K/MPD (1:1:1) 37.5%, MES/imidazole 0.1M pH 6.5, Morpheus Halides 90 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→65.57 Å / Num. obs: 7339 / % possible obs: 99.24 % / Redundancy: 3.3 % / CC1/2: 0.981 / Rrim(I) all: 0.124 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.87→1.9 Å / Num. unique obs: 282 / CC1/2: 0.596 / Rrim(I) all: 0.434 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→37.26 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.62 / 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 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→37.26 Å
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Refine LS restraints |
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LS refinement shell |
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