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Yorodumi- PDB-4m8z: Crystal Structure of SFH3, a phosphatidylinositol transfer protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m8z | ||||||
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Title | Crystal Structure of SFH3, a phosphatidylinositol transfer protein that integrates phosphoinositide signaling with lipid droplet metabolism | ||||||
Components | Phosphatidylinositol transfer protein PDR16 | ||||||
Keywords | SIGNALING PROTEIN / Lipid droplets / Phosphoinositides / meiosis / CRAL TRIO / SEC14 / phospholipid signaling | ||||||
Function / homology | Function and homology information negative regulation of sexual sporulation resulting in formation of a cellular spore / phosphatidylinositol transporter complex / phosphatidylinositol transfer activity / nucleus-vacuole junction / sterol binding / sterol biosynthetic process / phospholipid biosynthetic process / phospholipid transport / lipid droplet / cell periphery ...negative regulation of sexual sporulation resulting in formation of a cellular spore / phosphatidylinositol transporter complex / phosphatidylinositol transfer activity / nucleus-vacuole junction / sterol binding / sterol biosynthetic process / phospholipid biosynthetic process / phospholipid transport / lipid droplet / cell periphery / response to xenobiotic stimulus / endoplasmic reticulum membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.928 Å | ||||||
Authors | Ortlund, E.O. / Pathak, M.C. | ||||||
Citation | Journal: Mol Biol Cell / Year: 2014 Title: A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis. Authors: Ren, J. / Pei-Chen Lin, C. / Pathak, M.C. / Temple, B.R. / Nile, A.H. / Mousley, C.J. / Duncan, M.C. / Eckert, D.M. / Leiker, T.J. / Ivanova, P.T. / Myers, D.S. / Murphy, R.C. / Brown, H.A. ...Authors: Ren, J. / Pei-Chen Lin, C. / Pathak, M.C. / Temple, B.R. / Nile, A.H. / Mousley, C.J. / Duncan, M.C. / Eckert, D.M. / Leiker, T.J. / Ivanova, P.T. / Myers, D.S. / Murphy, R.C. / Brown, H.A. / Verdaasdonk, J. / Bloom, K.S. / Ortlund, E.A. / Neiman, A.M. / Bankaitis, V.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m8z.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m8z.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 4m8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/4m8z ftp://data.pdbj.org/pub/pdb/validation_reports/m8/4m8z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 41013.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c Gene: N1158, NP_014168.1. NM_001183069.1, PDR16, SFH3, YNL231C Plasmid: pGEM_SFH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P53860 #2: 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: 2.66 Å3/Da / Density % sol: 53.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: The reservoir solution consisted of 15 - 30% PEG 4000, 5% glycerol, 100 mM ammonium sulfate, 100 mM ammonium acetate pH 5.6. Thin plate-like crystals were harvested 3 - 4 days after mixing 2 ...Details: The reservoir solution consisted of 15 - 30% PEG 4000, 5% glycerol, 100 mM ammonium sulfate, 100 mM ammonium acetate pH 5.6. Thin plate-like crystals were harvested 3 - 4 days after mixing 2 ul protein solution (5 mg/ml) with 2 ul reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9782 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→89.89 Å / Num. all: 66699 / Num. obs: 66699 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.928→28.427 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.21 / σ(F): 43.72 / Phase error: 29.47 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.838 Å2
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Refinement step | Cycle: LAST / Resolution: 1.928→28.427 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 20681 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell |
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