[English] 日本語
Yorodumi- PDB-3oa7: Structure of the C-terminal domain of Cnm67, a core component of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oa7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the C-terminal domain of Cnm67, a core component of the spindle pole body of Saccharomyces cerevisiae | ||||||
Components | Head morphogenesis protein, Chaotic nuclear migration protein 67 fusion protein | ||||||
Keywords | STRUCTURAL PROTEIN / coiled coils / spindle pole body | ||||||
Function / homology | Function and homology information outer plaque of mitotic spindle pole body / spindle pole body organization / outer plaque of spindle pole body / viral scaffold / spindle pole body / sporulation resulting in formation of a cellular spore / virion assembly / mitotic spindle organization / meiotic cell cycle / structural constituent of cytoskeleton ...outer plaque of mitotic spindle pole body / spindle pole body organization / outer plaque of spindle pole body / viral scaffold / spindle pole body / sporulation resulting in formation of a cellular spore / virion assembly / mitotic spindle organization / meiotic cell cycle / structural constituent of cytoskeleton / cell division / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Klenchin, V.A. / Frye, J.J. / Rayment, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure-function analysis of the C-terminal domain of CNM67, a core component of the Saccharomyces cerevisiae spindle pole body. Authors: Klenchin, V.A. / Frye, J.J. / Jones, M.H. / Winey, M. / Rayment, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3oa7.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3oa7.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/3oa7 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/3oa7 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 24281.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: 7, CNM67, YNL225C, N1264 / Production host: Escherichia coli (E. coli) / References: UniProt: P13848, UniProt: P53865 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 10% monomethyl PEG 5000, 1.0M tetramethyl ammonium chloride, 100 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 16, 2007 |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 14536 / Num. obs: 14536 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 13.059 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.842 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|