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Yorodumi- PDB-4ph7: Structure of Osh6p in complex with phosphatidylinositol 4-phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ph7 | |||||||||
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Title | Structure of Osh6p in complex with phosphatidylinositol 4-phosphate | |||||||||
Components | Oxysterol-binding protein homolog 6 | |||||||||
Keywords | LIPID TRANSPORT / Transport Protein / Osh proteins Phosphatidylinositol Phosphate Lipid transport | |||||||||
Function / homology | Function and homology information Acyl chain remodelling of PS / sterol transfer activity / sterol homeostasis / sterol transport / sterol binding / phospholipid transporter activity / phosphatidylinositol-5-phosphate binding / cortical endoplasmic reticulum / sterol metabolic process / maintenance of cell polarity ...Acyl chain remodelling of PS / sterol transfer activity / sterol homeostasis / sterol transport / sterol binding / phospholipid transporter activity / phosphatidylinositol-5-phosphate binding / cortical endoplasmic reticulum / sterol metabolic process / maintenance of cell polarity / phosphatidic acid binding / phospholipid transport / piecemeal microautophagy of the nucleus / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / phosphatidylserine binding / exocytosis / endocytosis / lipid binding / endoplasmic reticulum membrane / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Delfosse, V. / Moser von Filseck, J. / Antonny, B. / Bourguet, W. / Drin, G. | |||||||||
Funding support | France, 2items
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Citation | Journal: Science / Year: 2015 Title: INTRACELLULAR TRANSPORT. Phosphatidylserine transport by ORP/Osh proteins is driven by phosphatidylinositol 4-phosphate. Authors: Moser von Filseck, J. / Copic, A. / Delfosse, V. / Vanni, S. / Jackson, C.L. / Bourguet, W. / Drin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ph7.cif.gz | 341.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ph7.ent.gz | 273.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ph7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ph7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ph7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ph7_validation.xml.gz | 62.7 KB | Display | |
Data in CIF | 4ph7_validation.cif.gz | 85.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/4ph7 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/4ph7 | HTTPS FTP |
-Related structure data
Related structure data | 4b2zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 51809.020 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: OSH6, YKR003W, YK102 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02201 #2: Chemical | ChemComp-2Y5 / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.98 % / Description: Needles Urchins |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.5 Details: 200 mM Ammonium Acetate, 100 mM BisTris, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97298 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97298 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→48.56 Å / Num. obs: 77182 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.106 / Net I/σ(I): 15.65 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 4.95 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B2Z Resolution: 2.55→48.562 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 23.62 / 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: 2.55→48.562 Å
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Refine LS restraints |
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LS refinement shell |
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