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- PDB-7wvt: Crystal structure of Saccharomyces cerevisiae Sfh2 complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wvt | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Sfh2 complexed with phosphatidylinositol | ||||||
![]() | Phosphatidylinositol transfer protein CSR1 | ||||||
![]() | LIPID TRANSPORT / Sec14 / phosphatidylinositol / squalene / transport | ||||||
Function / homology | ![]() negative regulation of phosphatidylglycerol biosynthetic process / positive regulation of phosphatidylcholine biosynthetic process / phosphatidylinositol transfer activity / prospore membrane / phospholipid catabolic process / phosphatidylinositol metabolic process / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / Golgi to plasma membrane protein 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 / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / phospholipid transport / lipid droplet / endosome / endoplasmic reticulum / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, L. / Tan, L. / Im, Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 141.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 690.1 KB | Display | ![]() |
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Full document | ![]() | 696 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wwdC ![]() 7wweC ![]() 7wwgC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Details (production host): N-terminal thrombin cleavable hexahistidine-tag Production host: ![]() ![]() |
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#2: Chemical | ChemComp-B7N / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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