+Open data
-Basic information
Entry | Database: PDB / ID: 6fc6 | ||||||||||||
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Title | Bik1 CAP-Gly domain with ETF peptide from Bim1 | ||||||||||||
Components |
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Keywords | CELL CYCLE / +TIP / Bik1 / CAP-Gly / Bim1 / ETF / yeast | ||||||||||||
Function / homology | Function and homology information protein localization to microtubule plus-end / mitotic spindle orientation checkpoint signaling / 2-micrometer plasmid partitioning / nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / cell tip / nuclear migration along microtubule / protein localization to microtubule / microtubule plus-end ...protein localization to microtubule plus-end / mitotic spindle orientation checkpoint signaling / 2-micrometer plasmid partitioning / nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / cell tip / nuclear migration along microtubule / protein localization to microtubule / microtubule plus-end / negative regulation of microtubule depolymerization / microtubule plus-end binding / mating projection tip / spindle pole body / microtubule associated complex / microtubule organizing center / microtubule depolymerization / mitotic sister chromatid cohesion / negative regulation of microtubule polymerization / establishment of mitotic spindle orientation / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / spindle microtubule / mitotic spindle / spindle / kinetochore / spindle pole / cell cortex / microtubule binding / cell division / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Kumar, A. / Stangier, M.M. / Steinmetz, M.O. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Structure / Year: 2018 Title: Structure-Function Relationship of the Bik1-Bim1 Complex. Authors: Stangier, M.M. / Kumar, A. / Chen, X. / Farcas, A.M. / Barral, Y. / Steinmetz, M.O. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fc6.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fc6.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fc6 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fc6 | HTTPS FTP |
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-Related structure data
Related structure data | 6fc5SC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11357.175 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: BIK1, YCL029C, YCL29C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P11709 |
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#2: Protein/peptide | Mass: 1294.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40013 |
#3: 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: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.4 / Details: 0.1 M sodium cacodylate, 1.0 M sodium citrate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.55 Å / Num. obs: 8808 / % possible obs: 100 % / Redundancy: 25.3 % / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.87 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Bik1 CAP-Gly domain (PDB ID: 6FC5) Resolution: 1.8→40.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.768 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.129 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.75 Å2 / Biso mean: 33.25 Å2 / Biso min: 17.09 Å2
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Refinement step | Cycle: final / Resolution: 1.8→40.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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