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Open data
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Basic information
Entry | Database: PDB / ID: 7zga | ||||||
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Title | Structure of yeast Sec14p with ergoline | ||||||
![]() | SEC14 cytosolic factor | ||||||
![]() | LIPID BINDING PROTEIN / Sec14p / ergoline | ||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hong, Z. / Johnen, P. / Schaaf, G. / Bono, F. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134 KB | Display | ![]() |
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PDB format | ![]() | 103.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7zg9C ![]() 7zgbC ![]() 7zgcC ![]() 7zgdC ![]() 1auaS S: Starting model for refinement 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34017.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-IUF / ~{ |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % |
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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 adjusted to pH 7.0 |
-Data collection
Diffraction | Mean temperature: 124 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 2.3→44.529 Å / Num. obs: 41643 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rrim(I) all: 0.094 / Net I/σ(I): 13.02 |
Reflection shell | Resolution: 2.3→6.83 Å / Num. unique obs: 41643 / Rrim(I) all: 0.094 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1aua Resolution: 2.302→44.529 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7 / 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: 2.302→44.529 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.8216 Å / Origin y: 101.2479 Å / Origin z: 1.2943 Å
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Refinement TLS group | Selection details: all |