+Open data
-Basic information
Entry | Database: PDB / ID: 1ek0 | ||||||
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Title | GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION | ||||||
Components | PROTEIN (GTP-BINDING PROTEIN YPT51) | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / G PROTEIN / VESICULAR TRAFFIC / GTP HYDROLYSIS / YPT/RAB PROTEIN / ENDOCYTOSIS / HYDROLASE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / Golgi to endosome transport / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body assembly / reticulophagy / endocytic vesicle ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / Golgi to endosome transport / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body assembly / reticulophagy / endocytic vesicle / endomembrane system / Neutrophil degranulation / endocytosis / late endosome / mitochondrial outer membrane / early endosome / endosome membrane / GTPase activity / GTP binding / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Esters, H. / Scheidig, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis. Authors: Esters, H. / Alexandrov, K. / Constantinescu, A.T. / Goody, R.S. / Scheidig, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ek0.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ek0.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ek0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ek0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1ek0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ek0_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1ek0_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ek0 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ek0 | HTTPS FTP |
-Related structure data
Related structure data | 5p21S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18963.666 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P36017 |
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-Non-polymers , 5 types, 213 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-GNP / |
#5: Chemical | ChemComp-GDP / |
#6: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
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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 Å3/Da / Density % sol: 54.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG-3350, 100 MM HEPES, PH 7.5, 20 MM NICL2 , VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.903 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1999 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.903 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→20 Å / Num. all: 146199 / Num. obs: 33345 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 27.55 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.22 / Num. unique all: 5853 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 146199 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5P21 Resolution: 1.48→31 Å / Num. parameters: 660 / Num. restraintsaints: 610 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1609 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→31 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 31 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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