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Yorodumi- PDB-3b7q: Crystal Structure of Yeast Sec14 Homolog Sfh1 in Complex with Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b7q | ||||||
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Title | Crystal Structure of Yeast Sec14 Homolog Sfh1 in Complex with Phosphatidylcholine | ||||||
Components | Uncharacterized protein YKL091C | ||||||
Keywords | SIGNALING PROTEIN / Sec14 / Golgi / phospholipid / phosphatidylcholine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å | ||||||
Authors | Ortlund, E.A. / Schaaf, G. / Redinbo, M.R. / Bankaitis, V. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Functional anatomy of phospholipid binding and regulation of phosphoinositide homeostasis by proteins of the sec14 superfamily Authors: Schaaf, G. / Ortlund, E.A. / Tyeryar, K.R. / Mousley, C.J. / Ile, K.E. / Garrett, T.A. / Ren, J. / Woolls, M.J. / Raetz, C.R. / Redinbo, M.R. / 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 | 3b7q.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7q.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7q ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7q | HTTPS FTP |
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-Related structure data
Related structure data | 3b74SC 3b7nC 3b7zC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 37413.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: BY4741 / Plasmid: Pet28_SFH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P33324 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.72 Å3/Da / Density % sol: 54.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 15-25% PEG 3350, 5% glycerol, and either 100 mM ammonium sulfate or 100mM potassium phosphate, 100 mM ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2006 Details: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.03→50 Å / Num. obs: 50846 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Χ2: 1.315 / Net I/σ(I): 14.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: PDB entry 3B74 Resolution: 2.03→40.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 194481.297 / 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: 40.687 Å2 / ksol: 0.362 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→40.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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