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Yorodumi- PDB-1ocu: Crystal structure of the yeast PX-domain protein Grd19p (sorting ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ocu | ||||||
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Title | Crystal structure of the yeast PX-domain protein Grd19p (sorting nexin 3) complexed to phosphatidylinosytol-3-phosphate. | ||||||
Components | SORTING NEXIN | ||||||
Keywords | SORTING PROTEIN / YEAST PROTEIN / SORTING NEXIN / COMPLEX WITH PHOSPHATIDYLINOSITOL PHOSPHATE | ||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / endocytic recycling / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane / Ub-specific processing proteases / protein localization / protein transport ...WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / endocytic recycling / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane / Ub-specific processing proteases / protein localization / protein transport / early endosome membrane / endosome / Golgi membrane / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate. Authors: Zhou, C.Z. / Li de La Sierra-Gallay, I. / Quevillon-Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. ...Authors: Zhou, C.Z. / Li de La Sierra-Gallay, I. / Quevillon-Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henckes, 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 | 1ocu.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ocu.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ocu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ocu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1ocu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ocu_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1ocu_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1ocu ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1ocu | HTTPS FTP |
-Related structure data
Related structure data | 1ocsSC 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: 18876.814 Da / Num. of mol.: 2 / Fragment: PX-DOMAIN Source method: isolated from a genetically manipulated source Details: CHEMICALLY MODIFIED CYSTEINE. D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATE Source: (gene. exp.) Saccharomyces cerevisiae S288C / Description: CLONED GENE / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08826 #2: Chemical | #3: 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 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: 10% PEG8000, 8% ETHYLENE GLYCOL, 0.1M NA-HEPES PH 7,5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7 / 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: 0.984 |
Detector | Date: Jul 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→25 Å / Num. obs: 17289 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.28→2.33 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.2 / % possible all: 77.3 |
Reflection | *PLUS Highest resolution: 2.28 Å / Lowest resolution: 25.08 Å / Num. all: 65105 / Num. obs: 11970 / % possible obs: 95.97 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 77.31 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OCS Resolution: 2.3→20 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 1 A TO 27 A AND 162 A, 1B TO 30 B ARE ABSENT FROM THE FINAL MODEL BECAUSE DISORDERED.
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Displacement parameters | Biso mean: 41.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.32 Å / Total num. of bins used: 33 /
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 4.8 % / Rfactor Rwork: 0.222 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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