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Yorodumi- PDB-3b74: Crystal Structure of Yeast Sec14 Homolog Sfh1 in Complex with Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b74 | |||||||||
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Title | Crystal Structure of Yeast Sec14 Homolog Sfh1 in Complex with Phosphatidylethanolamine | |||||||||
Components | Uncharacterized protein YKL091C | |||||||||
Keywords | SIGNALING PROTEIN / Sec14 / Golgi / phospholipid / phosphatidylethanolamine | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3b74.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b74.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 3b74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b74 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b74 | HTTPS FTP |
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-Related structure data
Related structure data | 3b7nC 3b7qC 3b7zC 1auaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37413.758 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-PEE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25.5 % (w/v) PEG 4000, 15 % (w/v) glycerol (11.9 % (v/v) and170 mM potassium acetate, 85 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 27912 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.343 / Num. unique all: 2784 / Rsym value: 0.0103 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AUA Resolution: 1.9→40.87 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 850047.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.217 Å2 / ksol: 0.369331 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→40.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Total num. of bins used: 6
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Xplor file |
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