+Open data
-Basic information
Entry | Database: PDB / ID: 1yzn | ||||||
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Title | GppNHp-Bound Ypt1p GTPase | ||||||
Components | GTP-binding protein YPT1 | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Ypt1p GTPase / vesicular trafficking | ||||||
Function / homology | Function and homology information pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic ...pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-coated vesicle budding / COPII-mediated vesicle transport / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / phagophore assembly site membrane / Golgi stack / cis-Golgi network / endocytic recycling / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / reticulophagy / SNARE complex assembly / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / SNARE binding / macroautophagy / intracellular protein transport / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzn.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzn.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 1yzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzn ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzn | HTTPS FTP |
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-Related structure data
Related structure data | 1yu9C 1yvdC 1yzkC 1yzlC 1yzmC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 1z0aC 1z0dC 1z0fC 1z0iC 1z0jC 1z0kC 1z22C 1z2aC 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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Unit cell |
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-Components
#1: Protein | Mass: 21066.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YPT1, YP2 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL cells / References: UniProt: P01123 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: 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: 2.08 Å3/Da / Density % sol: 40.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% MPD, 10% Glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2003 / Details: osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. all: 10706 / Num. obs: 10705 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.068 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.06→2.12 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 880 / Rsym value: 0.293 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine Rab3A GTPase Resolution: 2.06→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.236 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.112 Å / Total num. of bins used: 20
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