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Yorodumi- PDB-4inq: Crystal structure of Osh3 ORD in complex with PI(4)P from Sacchar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4inq | ||||||
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Title | Crystal structure of Osh3 ORD in complex with PI(4)P from Saccharomyces cerevisiae | ||||||
Components | Oxysterol-binding protein homolog 3 | ||||||
Keywords | LIPID BINDING PROTEIN / beta barrel / lipid transport / PI(4)P | ||||||
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 / sterol transport / invasive growth in response to glucose limitation / : / sterol binding / ER to Golgi ceramide transport / perinuclear endoplasmic reticulum ...Synthesis of bile acids and bile salts / sterol transfer activity / pseudohyphal growth / karyogamy involved in conjugation with cellular fusion / sterol transport / invasive growth in response to glucose limitation / : / sterol binding / ER to Golgi ceramide transport / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / maintenance of cell polarity / piecemeal microautophagy of the nucleus / cholesterol binding / exocytosis / endocytosis / lipid binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 4inq.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4inq.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 4inq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4inq_validation.pdf.gz | 677.3 KB | Display | wwPDB validaton report |
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Full document | 4inq_full_validation.pdf.gz | 686.8 KB | Display | |
Data in XML | 4inq_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4inq_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4inq ftp://data.pdbj.org/pub/pdb/validation_reports/in/4inq | HTTPS FTP |
-Related structure data
Related structure data | 4iapC 4ic4SC 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: 45683.703 Da / Num. of mol.: 1 / Fragment: ORD (OSBP related domain), UNP residues 605-996 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: OSH3, YHR073W / Plasmid: modifed pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38713 |
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#2: Chemical | ChemComp-PIF / ( |
#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: 1.86 Å3/Da / Density % sol: 33.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES-NaOH, 25% polyethyleneglycol(PEG) 1500, 0.1M MgCl2, 0.5mM PI(4)P, pH 6.0, 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: Nov 25, 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: 2.2→50 Å / Num. all: 2 / Num. obs: 18011 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 5.25 / Num. unique all: 922 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IC4 Resolution: 2.2→40.35 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1454574.55 / 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: 36.6663 Å2 / ksol: 0.353025 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→40.35 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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