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Yorodumi- PDB-2gil: Structure of the extremely slow GTPase Rab6A in the GTP bound for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gil | ||||||
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Title | Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution | ||||||
Components | Ras-related protein Rab-6A | ||||||
Keywords | PROTEIN TRANSPORT / protein-nucleotide complex / GTPase-fold | ||||||
Function / homology | Function and homology information peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / intra-Golgi vesicle-mediated transport ...peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / intra-Golgi vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs / antigen processing and presentation / endomembrane system / localization / secretory granule membrane / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / neuron projection development / cytoplasmic vesicle / protein domain specific binding / Golgi membrane / GTPase activity / Neutrophil degranulation / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Bergbrede, T. / Pylypenko, O. / Rak, A. / Alexandrov, K. | ||||||
Citation | Journal: J.STRUCT.BIOL. / Year: 2005 Title: Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution Authors: Bergbrede, T. / Pylypenko, O. / Rak, A. / Alexandrov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gil.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gil.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 2gil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/2gil ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gil | HTTPS FTP |
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-Related structure data
Related structure data | 1d5cS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18619.230 Da / Num. of mol.: 4 / Fragment: Rab6aNd12Cd33 (residues 12-173) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20340 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GTP / #4: 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: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100mM TrisHCl, 1M LiCl, 32% (w/v) polyethylene glycol 1000, 3.3mM Nonyl-D-glucoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0398 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0398 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→19.05 Å / Num. all: 48538 / Num. obs: 48538 / % possible obs: 87.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 25.99 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.032 / Net I/σ(I): 17.44 |
Reflection shell | Resolution: 1.82→1.9 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3482 / Rsym value: 0.146 / % possible all: 52.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D5C Resolution: 1.82→19.05 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.878 / SU B: 3.892 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.187 / Stereochemistry target values: Engh & Huber
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.728 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→19.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Total num. of bins used: 20
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