+Open data
-Basic information
Entry | Database: PDB / ID: 1vg1 | ||||||
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Title | GDP-Bound Rab7 | ||||||
Components | Ras-related protein Rab-7 | ||||||
Keywords | PROTEIN TRANSPORT / GTP-binding protein | ||||||
Function / homology | Function and homology information RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / RHOD GTPase cycle / lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / RHOG GTPase cycle / RAC2 GTPase cycle ...RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / RHOD GTPase cycle / lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / RHOG GTPase cycle / RAC2 GTPase cycle / : / RHOH GTPase cycle / protein to membrane docking / RHOQ GTPase cycle / RAB geranylgeranylation / RAC1 GTPase cycle / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / MHC class II antigen presentation / retromer complex / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / early endosome to late endosome transport / positive regulation of exosomal secretion / retrograde transport, endosome to Golgi / Neutrophil degranulation / endosome to lysosome transport / autophagosome membrane / autophagosome assembly / intracellular transport / viral release from host cell / lipid catabolic process / phagocytic vesicle / bone resorption / lipid droplet / small monomeric GTPase / G protein activity / mitochondrial membrane / response to bacterium / terminal bouton / synaptic vesicle membrane / small GTPase binding / phagocytic vesicle membrane / GDP binding / positive regulation of protein catabolic process / late endosome / late endosome membrane / lysosome / endosome membrane / endosome / lysosomal membrane / GTPase activity / GTP binding / Golgi apparatus / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease Authors: Rak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vg1.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vg1.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/1vg1 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/1vg1 | HTTPS FTP |
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-Related structure data
Related structure data | 1vg0SC 1vg8C 1vg9C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21120.998 Da / Num. of mol.: 1 / Fragment: Gtpase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09527 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#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: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 25% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 2, 2002 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.8 Å / Num. all: 13877 / Num. obs: 13877 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 1929 / Rsym value: 0.322 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Rab7 from REP1:Rab7 complex (PDB code 1VG0) Resolution: 1.9→18.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2358514.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.5484 Å2 / ksol: 0.380535 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→18.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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