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Yorodumi- PDB-4iap: Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iap | ||||||
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Title | Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae | ||||||
Components | Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3 | ||||||
Keywords | LIPID BINDING PROTEIN/ HYDRORASE / PH domain / beta sandwitch / targeting / phosphoinositides / LIPID BINDING PROTEIN- HYDRORASE complex | ||||||
Function / homology | Function and homology information Synthesis of bile acids and bile salts / sterol transfer activity / pseudohyphal growth / karyogamy involved in conjugation with cellular fusion / ER to Golgi ceramide transport / invasive growth in response to glucose limitation / sterol transport / sterol binding / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum ...Synthesis of bile acids and bile salts / sterol transfer activity / pseudohyphal growth / karyogamy involved in conjugation with cellular fusion / ER to Golgi ceramide transport / invasive growth in response to glucose limitation / sterol transport / sterol binding / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / maintenance of cell polarity / piecemeal microautophagy of the nucleus / reticulophagy / exocytosis / viral release from host cell by cytolysis / peptidoglycan catabolic process / endocytosis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / lipid binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tong, J. / Im, Y.J. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure of osh3 reveals a conserved mode of phosphoinositide binding in oxysterol-binding proteins Authors: Tong, J. / Yang, H. / Yang, H. / Eom, S.H. / Im, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iap.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iap.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 4iap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iap_validation.pdf.gz | 451.6 KB | Display | wwPDB validaton report |
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Full document | 4iap_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 4iap_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4iap_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/4iap ftp://data.pdbj.org/pub/pdb/validation_reports/ia/4iap | HTTPS FTP |
-Related structure data
Related structure data | 4ic4C 4inqC 212lS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29746.031 Da / Num. of mol.: 2 Fragment: PH domain (UNP residues 221-317), T4 Lysozyme (UNP residues 2-161),PH domain (UNP residues 237-315) Mutation: D1020N, C1054T, C1097A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus) Strain: ATCC 204508 / S288c / Gene: OSH3, YHR073W / Plasmid: modifed pHIS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38713, UniProt: P00720, lysozyme #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THERE ARE SEQUENCE CONFLICTS IN THE UNP SEQUENCE REFERENCE P00720. | |
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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: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, 15% PEG8000, 0.2 M Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 33493 / Num. obs: 32983 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1666 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T4 Lysozyme 212L Resolution: 2.3→40.02 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1788889.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.8257 Å2 / ksol: 0.328213 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→40.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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