+Open data
-Basic information
Entry | Database: PDB / ID: 2y8e | ||||||
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Title | Crystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP | ||||||
Components | RAB-PROTEIN 6 | ||||||
Keywords | HYDROLASE / NUCLEOTIDE BINDING / GTP BINDING | ||||||
Function / homology | Function and homology information Intra-Golgi traffic / TBC/RABGAPs / RAB geranylgeranylation / germarium-derived egg chamber formation / R7 cell development / oocyte microtubule cytoskeleton polarization / compound eye morphogenesis / pole plasm oskar mRNA localization / COPI-independent Golgi-to-ER retrograde traffic / Rab protein signal transduction ...Intra-Golgi traffic / TBC/RABGAPs / RAB geranylgeranylation / germarium-derived egg chamber formation / R7 cell development / oocyte microtubule cytoskeleton polarization / compound eye morphogenesis / pole plasm oskar mRNA localization / COPI-independent Golgi-to-ER retrograde traffic / Rab protein signal transduction / receptor recycling / Neutrophil degranulation / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / exocytosis / phototransduction / autophagosome / regulation of postsynaptic membrane potential / endomembrane system / defense response to fungus / vesicle-mediated transport / axon guidance / intracellular protein transport / actin binding / cytoplasmic vesicle / perikaryon / lysosome / Golgi membrane / GTPase activity / neuronal cell body / synapse / GTP binding / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Walden, M. / Edwards, T.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structure of the Drosophila Melanogaster Rab6 Gtpase at 1.4 A Resolution Authors: Walden, M. / Jenkins, H.T. / Edwards, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y8e.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y8e.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y8e ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y8e | HTTPS FTP |
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-Related structure data
Related structure data | 1yzqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.97427, 0.11653, 0.19292), Vector: |
-Components
#1: Protein | Mass: 20343.035 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O18334 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 1.92 Å3/Da / Density % sol: 35 % / Description: NONE |
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Crystal grow | pH: 8 Details: 2.4 M AMMONIUM SULPHATE, 0.1 M IMIDAZOLE PH 8.0, 2.5% PEG 400, 2.5% DMSO AND 3% TRIMETHYLAMINE N-OXIDE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→31.7 Å / Num. obs: 61395 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.326 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.4 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YZQ Resolution: 1.39→63.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.7 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.573 Å2
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Refinement step | Cycle: LAST / Resolution: 1.39→63.4 Å
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Refine LS restraints |
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