+Open data
-Basic information
Entry | Database: PDB / ID: 6fc5 | ||||||||||||
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Title | Bik1 CAP-Gly domain | ||||||||||||
Components | Microtubule-associated protein | ||||||||||||
Keywords | CELL CYCLE / +TIP / CAP-Gly / microtubule / yeast | ||||||||||||
Function / homology | Function and homology information 2-micrometer plasmid partitioning / nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / cell tip / microtubule plus-end / mating projection tip / microtubule plus-end binding / spindle pole body / microtubule associated complex ...2-micrometer plasmid partitioning / nuclear migration involved in conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / cell tip / microtubule plus-end / mating projection tip / microtubule plus-end binding / spindle pole body / microtubule associated complex / negative regulation of microtubule polymerization / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / spindle microtubule / kinetochore / spindle / 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: 1.88 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 | 6fc5.cif.gz | 30.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fc5.ent.gz | 19.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fc5_validation.pdf.gz | 415.3 KB | Display | wwPDB validaton report |
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Full document | 6fc5_full_validation.pdf.gz | 415.3 KB | Display | |
Data in XML | 6fc5_validation.xml.gz | 6 KB | Display | |
Data in CIF | 6fc5_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fc5 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fc5 | HTTPS FTP |
-Related 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 Details: GPMDRYQRKIGCFIQIPNLGRGQLKYVGPVDTKAGMFAGVDLLANIGKNDGSFMGKKYFQTE YPQSGLFIQLQKVASLIEKASISQTSRRTTMEPLSIPKNR Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BIK1, SCKG_5419 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A250WN99, UniProt: P11709*PLUS |
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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: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / 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: Aug 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→40.4 Å / Num. obs: 7731 / % possible obs: 99.8 % / Redundancy: 25 % / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.88→1.95 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→40.4 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.737 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.122 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: 88.45 Å2 / Biso mean: 34.056 Å2 / Biso min: 16.68 Å2
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Refinement step | Cycle: final / Resolution: 1.88→40.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.883→1.931 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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