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Yorodumi- PDB-7wvt: Crystal structure of Saccharomyces cerevisiae Sfh2 complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wvt | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Sfh2 complexed with phosphatidylinositol | ||||||
Components | Phosphatidylinositol transfer protein CSR1 | ||||||
Keywords | LIPID TRANSPORT / Sec14 / phosphatidylinositol / squalene / transport | ||||||
Function / homology | Function and homology information negative regulation of phosphatidylglycerol biosynthetic process / positive regulation of phosphatidylcholine biosynthetic process / phosphatidylinositol transfer activity / prospore membrane / phospholipid catabolic process / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / phospholipid transport ...negative regulation of phosphatidylglycerol biosynthetic process / positive regulation of phosphatidylcholine biosynthetic process / phosphatidylinositol transfer activity / prospore membrane / phospholipid catabolic process / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / phospholipid transport / lipid droplet / endosome / endoplasmic reticulum / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Chen, L. / Tan, L. / Im, Y.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Structural basis of ligand recognition and transport by Sfh2, a yeast phosphatidylinositol transfer protein of the Sec14 superfamily. Authors: Chen, L. / Tan, L. / 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 | 7wvt.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wvt.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/7wvt ftp://data.pdbj.org/pub/pdb/validation_reports/wv/7wvt | HTTPS FTP |
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-Related structure data
Related structure data | 7wwdC 7wweC 7wwgC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46570.641 Da / Num. of mol.: 1 / Mutation: deletion of loop residues (44-49 and 61-66) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: CSR1, SFH2, YLR380W / Plasmid: pHIS2-Thr Details (production host): N-terminal thrombin cleavable hexahistidine-tag Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06705 |
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#2: Chemical | ChemComp-B7N / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 38.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 30% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 59663 / % possible obs: 98 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 2577 / CC1/2: 0.898 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.77 Å / SU ML: 0.1423 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2086 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: AlphaFold model Q06705 was used as the starting model.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→28.77 Å
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Refine LS restraints |
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LS refinement shell |
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