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Yorodumi- PDB-2iey: Crystal Structure of mouse Rab27b bound to GDP in hexagonal space... -
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-Basic information
Entry | Database: PDB / ID: 2iey | ||||||
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Title | Crystal Structure of mouse Rab27b bound to GDP in hexagonal space group | ||||||
Components | Ras-related protein Rab-27B | ||||||
Keywords | SIGNALING PROTEIN / Rab27 / GTPase / Rab / GDP / swapping | ||||||
Function / homology | Function and homology information RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / exocytic vesicle / Golgi stack / multivesicular body sorting pathway / myosin V binding / trans-Golgi network transport vesicle ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / exocytic vesicle / Golgi stack / multivesicular body sorting pathway / myosin V binding / trans-Golgi network transport vesicle / regulation of exocytosis / multivesicular body membrane / exocytosis / positive regulation of exocytosis / synaptic vesicle endocytosis / axon cytoplasm / small monomeric GTPase / G protein activity / secretory granule / synaptic vesicle membrane / GDP binding / melanosome / late endosome / apical plasma membrane / protein domain specific binding / GTPase activity / GTP binding / Golgi apparatus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.18 Å | ||||||
Authors | Chavas, L.M.G. / Torii, S. / Kamikubo, H. / Kawasaki, M. / Ihara, K. / Kato, R. / Kataoka, M. / Izumi, T. / Wakatsuki, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure of the small GTPase Rab27b shows an unexpected swapped dimer Authors: Chavas, L.M.G. / Torii, S. / Kamikubo, H. / Kawasaki, M. / Ihara, K. / Kato, R. / Kataoka, M. / Izumi, T. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iey.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iey.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 2iey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2iey ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2iey | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological unit is a monomer. There are 2 biological units in the asymmetric unit (chain A and chain B) |
-Components
#1: Protein | Mass: 22495.502 Da / Num. of mol.: 2 / Fragment: soluble domain / Mutation: Q78L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q99P58, small monomeric GTPase #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: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: PEG 10000, Hepes, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUAMTUM 4r / Detector: CCD / Date: Nov 22, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→63.37 Å / Num. obs: 9142 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.8 % / Rmerge(I) obs: 0.111 / Χ2: 2.03 |
Reflection shell | Resolution: 3.18→3.31 Å / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.693 / Num. measured obs: 1554 / Num. unique all: 1554 / Χ2: 1.645 / % possible all: 100 |
-Phasing
Phasing | Method: SAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Phasing dm | FOM : 0.69 / FOM acentric: 0.71 / FOM centric: 0.66 / Reflection: 8389 / Reflection acentric: 6062 / Reflection centric: 2327 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.18→36.5 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.842 / SU B: 34.386 / SU ML: 0.562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.632 / 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: 43.356 Å2
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Refinement step | Cycle: LAST / Resolution: 3.18→36.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.183→3.265 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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