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Yorodumi- PDB-1zhy: Structure of yeast oxysterol binding protein Osh4 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zhy | ||||||
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Title | Structure of yeast oxysterol binding protein Osh4 in complex with cholesterol | ||||||
Components | KES1 protein | ||||||
Keywords | LIPID BINDING PROTEIN / oxysterol / sterol binding protein | ||||||
Function / homology | Function and homology information Acyl chain remodelling of PS / sterol transfer activity / sterol transport / : / ER to Golgi ceramide transport / post-Golgi vesicle-mediated transport / maintenance of cell polarity / piecemeal microautophagy of the nucleus / sphingolipid metabolic process / phosphatidic acid binding ...Acyl chain remodelling of PS / sterol transfer activity / sterol transport / : / ER to Golgi ceramide transport / post-Golgi vesicle-mediated transport / maintenance of cell polarity / piecemeal microautophagy of the nucleus / sphingolipid metabolic process / phosphatidic acid binding / oxysterol binding / phosphatidylinositol-4-phosphate binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / endocytosis / Golgi membrane / intracellular membrane-bounded organelle / lipid binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Im, Y.J. / Raychaudhuri, S. / Prinz, W.A. / Hurley, J.H. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural mechanism for sterol sensing and transport by OSBP-related proteins Authors: Im, Y.J. / Raychaudhuri, S. / Prinz, W.A. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zhy.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zhy.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/1zhy ftp://data.pdbj.org/pub/pdb/validation_reports/zh/1zhy | HTTPS FTP |
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-Related structure data
Related structure data | 1zhtC 1zhwC 1zhxSC 1zhzC 1zi7C C: citing same article (ref.) S: Starting model for refinement |
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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: 49898.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OSH4 / Plasmid: modified pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35844 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CLR / | #4: 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: 2.6 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 / Wavelength: 0.9792 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 6, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 67097 / Num. obs: 65109 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 3.6 / Num. unique all: 6094 / Rsym value: 0.255 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZHX Resolution: 1.6→36.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1430971.44 / 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: 41.0183 Å2 / ksol: 0.362261 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→36.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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