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Yorodumi- PDB-1pi6: YEAST ACTIN INTERACTING PROTEIN 1 (Aip1), ORTHORHOMBIC CRYSTAL FORM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pi6 | ||||||
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Title | YEAST ACTIN INTERACTING PROTEIN 1 (Aip1), ORTHORHOMBIC CRYSTAL FORM | ||||||
Components | Actin interacting protein 1 | ||||||
Keywords | PROTEIN BINDING / WD repeat / beta-propeller | ||||||
Function / homology | Function and homology information negative regulation of cytokinesis / actin cortical patch / Platelet degranulation / mating projection tip / actin filament depolymerization / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament / actin filament binding / actin binding ...negative regulation of cytokinesis / actin cortical patch / Platelet degranulation / mating projection tip / actin filament depolymerization / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament / actin filament binding / actin binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Voegtli, W.C. / Madrona, A.Y. / Wilson, D.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The structure of Aip1p, a WD repeat protein that regulates Cofilin-mediated actin depolymerization. Authors: Voegtli, W.C. / Madrona, A.Y. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pi6.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pi6.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pi6_validation.pdf.gz | 369.2 KB | Display | wwPDB validaton report |
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Full document | 1pi6_full_validation.pdf.gz | 390.1 KB | Display | |
Data in XML | 1pi6_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 1pi6_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/1pi6 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/1pi6 | HTTPS FTP |
-Related structure data
Related structure data | 1pguSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 67415.289 Da / Num. of mol.: 1 / Mutation: H530R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: AIP1 OR YMR092C OR YM9582.17C / Plasmid: pTyb4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P46680 |
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#2: Chemical | ChemComp-ZN / |
#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: 2.46 Å3/Da / Density % sol: 49.97 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG 4000, 100mM NaCl, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 23703 / Num. obs: 21676 / % possible obs: 91.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 22.9 Å2 |
Reflection shell | Resolution: 2.5→2.66 Å / % possible all: 80.6 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. obs: 22190 / % possible obs: 93.5 % / Num. measured all: 192575 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS Lowest resolution: 2.54 Å / % possible obs: 83.5 % / Rmerge(I) obs: 0.235 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PGU Resolution: 2.5→24.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 434259.93 / Data cutoff high rms absF: 434259.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.5035 Å2 / ksol: 0.3143 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→24.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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