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Yorodumi- PDB-1ocs: Crystal structure of the yeast PX-doamin protein Grd19p (sorting ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ocs | ||||||
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Title | Crystal structure of the yeast PX-doamin protein Grd19p (sorting nexin3) complexed to phosphatidylinosytol-3-phosphate. | ||||||
Components | SORTING NEXIN GRD19 | ||||||
Keywords | SORTING PROTEIN / SORTING NEXIN / PX-DOMAIN / YEAST PROTEIN | ||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / fungal-type vacuole membrane / protein localization / protein transport / early endosome membrane ...WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / fungal-type vacuole membrane / protein localization / protein transport / early endosome membrane / endosome / Golgi membrane / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.03 Å | ||||||
Authors | Zhou, C.Z. / Li De La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. ...Zhou, C.Z. / Li De La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / De La Torre, F. / Poupon, A. / Janin, J. / Van Tilbeurgh, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure of the Yeast Phox Homology (Px) Protein Grd19P (Sorting Nexin 3) Complexed to Phosphatidylinositol-3-Phosphate Authors: Zhou, C.Z. / Li De La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / De La ...Authors: Zhou, C.Z. / Li De La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / De La Torre, F. / Poupon, A. / Janin, J. / Van Tilbeurgh, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ocs.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ocs.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ocs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1ocs ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1ocs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18876.814 Da / Num. of mol.: 1 / Fragment: PX-DOMAIN, RESIDUES 1-162 Source method: isolated from a genetically manipulated source Details: CYSTEINE A91 CHEMICALLY MODIFIED BY BETA MERCAPTO-ETHANOL Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Description: CLONED GENE / Plasmid: PET9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08826 |
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#2: Chemical | ChemComp-GOL / |
#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: 2.23 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.8 / Details: 16% PEG 4000, 0.1M NA-HEPES PH7,5, pH 6.80 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797,0.9803,0.98,0.9825 | |||||||||||||||
Detector | Date: Feb 15, 2002 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.03→25 Å / Num. obs: 11970 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.6 | |||||||||||||||
Reflection shell | Resolution: 2.03→2.08 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 / % possible all: 98.1 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2.03 Å / Lowest resolution: 25 Å / Num. obs: 17289 / Redundancy: 5.1 % / Num. measured all: 60571 / Rmerge(I) obs: 0.065 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 98.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.03→20 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: REGION 1 A TO 29 A HAS BEEN OMITTED FROM THE FINAL MODEL BECAUSE DISORDERED.
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Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.09 Å / Total num. of bins used: 12 /
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 4.8 % / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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