+Open data
-Basic information
Entry | Database: PDB / ID: 7zg9 | ||||||
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Title | Structure of yeast Sec14p with himbacine | ||||||
Components | SEC14 cytosolic factor | ||||||
Keywords | LIPID BINDING PROTEIN / Sec14p / himbacine | ||||||
Function / homology | Function and homology information negative regulation of phosphatidylcholine biosynthetic process / negative regulation of phosphatidylglycerol biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport ...negative regulation of phosphatidylcholine biosynthetic process / negative regulation of phosphatidylglycerol biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport / Golgi membrane / Golgi apparatus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å | ||||||
Authors | Hong, Z. / Johnen, P. / Schaaf, G. / Bono, F. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Mechanisms by which small molecules of diverse chemotypes arrest Sec14 lipid transfer activity. Authors: Chen, X.R. / Poudel, L. / Hong, Z. / Johnen, P. / Katti, S. / Tripathi, A. / Nile, A.H. / Green, S.M. / Khan, D. / Schaaf, G. / Bono, F. / Bankaitis, V.A. / Igumenova, T.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zg9.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zg9.ent.gz | 206.1 KB | Display | PDB format |
PDBx/mmJSON format | 7zg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/7zg9 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/7zg9 | HTTPS FTP |
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-Related structure data
Related structure data | 7zgaC 7zgbC 7zgcC 7zgdC 1auaS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33962.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SEC14, PIT1, YMR079W, YM9582.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P24280 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 294 K / Method: evaporation Details: 129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 238 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→43.297 Å / Num. obs: 122833 / % possible obs: 100 % / Redundancy: 10.1 % / Rrim(I) all: 0.072 / Net I/σ(I): 19.16 |
Reflection shell | Resolution: 1.76→5.26 Å / Num. unique obs: 122833 / Rrim(I) all: 0.072 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1aua Resolution: 1.764→43.297 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.764→43.297 Å
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Refine LS restraints |
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LS refinement shell |
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