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Yorodumi- PDB-3okq: Crystal structure of a core domain of yeast actin nucleation cofa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3okq | ||||||
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Title | Crystal structure of a core domain of yeast actin nucleation cofactor Bud6 | ||||||
Components | Bud site selection protein 6 | ||||||
Keywords | PROTEIN BINDING / coiled-coil | ||||||
Function / homology | Function and homology information cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity ...cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / positive regulation of actin nucleation / cell tip / astral microtubule organization / incipient cellular bud site / cellular bud tip / cellular bud neck / mating projection tip / cellular hyperosmotic response / spindle pole body / establishment of cell polarity / actin filament bundle assembly / enzyme activator activity / regulation of actin cytoskeleton organization / regulation of protein localization / actin binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.044 Å | ||||||
Authors | Tu, D. / Eck, M.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structure of the formin-interaction domain of the actin nucleation-promoting factor Bud6. Authors: Tu, D. / Graziano, B.R. / Park, E. / Zheng, W. / Li, Y. / Goode, B.L. / Eck, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3okq.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3okq.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 3okq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3okq_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 3okq_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 3okq_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 3okq_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/3okq ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3okq | HTTPS FTP |
-Related structure data
Related structure data | 3onxSC 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: 16355.493 Da / Num. of mol.: 1 / Fragment: coiled-coil domain (unp residues 549-688) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: AIP3, BUD6, L8543.5, YLR319C / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P41697 |
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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: 3.03 Å3/Da / Density % sol: 59.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG 3350, 175 mM sodium malonate (pH 7.0), 20% glycerol, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2008 |
Radiation | Monochromator: MD2 microdiffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 12868 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.04→2.11 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1229 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3ONX Resolution: 2.044→35.394 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.29 / 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 / Bsol: 42.505 Å2 / ksol: 0.379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.044→35.394 Å
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Refine LS restraints |
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LS refinement shell |
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