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Yorodumi- PDB-8pv0: Crystal structure of tropomyosin (Cdc8) cables, Conformers 2 and 3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pv0 | ||||||
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Title | Crystal structure of tropomyosin (Cdc8) cables, Conformers 2 and 3 | ||||||
Components | Tropomyosin | ||||||
Keywords | STRUCTURAL PROTEIN / Tropomyosin / cdc8 / yeast / overlap complex | ||||||
Function / homology | Function and homology information plasma membrane fusion involved in cytogamy / formin-nucleated actin cable / mating projection actin fusion focus / RHOV GTPase cycle / actin lateral binding / actin cortical patch organization / mitotic actomyosin contractile ring assembly / mitotic actomyosin contractile ring / actomyosin contractile ring / actin cortical patch ...plasma membrane fusion involved in cytogamy / formin-nucleated actin cable / mating projection actin fusion focus / RHOV GTPase cycle / actin lateral binding / actin cortical patch organization / mitotic actomyosin contractile ring assembly / mitotic actomyosin contractile ring / actomyosin contractile ring / actin cortical patch / mitotic actomyosin contractile ring contraction / mating projection tip / cell division site / mitotic cytokinesis / actin filament / actin filament organization / actin filament binding / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å | ||||||
Authors | Reinke, P.Y.A. / Zahn, M. / Fedorov, R. / Manstein, D.J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Atomic structure of tropomyosin cables Authors: Reinke, P.Y.A. / Manstein, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pv0.cif.gz | 324.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pv0.ent.gz | 224.1 KB | Display | PDB format |
PDBx/mmJSON format | 8pv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pv0_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 8pv0_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 8pv0_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 8pv0_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/8pv0 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/8pv0 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19182.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: cdc8, SPAC27F1.02c / Production host: Escherichia coli (E. coli) / References: UniProt: Q02088 #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.8 Details: 10 mM Tris HCl pH 7.8, 0.15 M ammonium acetate, and 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9797 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2017 |
Radiation | Monochromator: 0.9797 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→107.93 Å / Num. obs: 28799 / % possible obs: 98.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 49.68 Å2 / CC1/2: 0.887 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.4→2.5 Å / Num. unique obs: 2178 / CC1/2: 0.887 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.43→53.97 Å / SU ML: 0.4608 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.5573 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→53.97 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 59.0014265954 Å / Origin y: 67.4893369429 Å / Origin z: 18.9674726022 Å
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Refinement TLS group | Selection details: all |