+Open data
-Basic information
Entry | Database: PDB / ID: 4f4b | ||||||
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Title | Structure of OSH4 with a cholesterol analog | ||||||
Components | Protein KES1 | ||||||
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: 1.87 Å | ||||||
Authors | Koag, M.C. / Monzingo, A.F. / Cheun, Y. / Lee, S. | ||||||
Citation | Journal: Steroids / Year: 2013 Title: Synthesis and structure of 16,22-diketocholesterol bound to oxysterol-binding protein Osh4. Authors: Koag, M.C. / Cheun, Y. / Kou, Y. / Ouzon-Shubeita, H. / Min, K. / Monzingo, A.F. / Lee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f4b.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f4b.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 4f4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/4f4b ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f4b | HTTPS FTP |
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-Related 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: 49770.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: KES1, OSH4, YPL145C, LPI3C, P2614 / Production host: Escherichia coli (E. coli) / References: UniProt: P35844 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8% PEG 20,000, 50 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→80.25 Å / Num. obs: 81133 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.059 / Χ2: 1.385 / Net I/σ(I): 9.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.2525 / WRfactor Rwork: 0.1996 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7841 / SU B: 4.308 / SU ML: 0.123 / SU R Cruickshank DPI: 0.175 / SU Rfree: 0.1711 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 214.47 Å2 / Biso mean: 22.8446 Å2 / Biso min: 7.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.923 Å / Total num. of bins used: 20
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