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Yorodumi- PDB-2fe4: The crystal structure of human neuronal Rab6B in its inactive GDP... -
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-Basic information
Entry | Database: PDB / ID: 2fe4 | ||||||
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Title | The crystal structure of human neuronal Rab6B in its inactive GDP-bound form | ||||||
Components | Ras-related protein Rab-6B | ||||||
Keywords | HYDROLASE / protein-nucleotide complex | ||||||
Function / homology | Function and homology information protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / 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 ...protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / 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 / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endomembrane system / small monomeric GTPase / intracellular protein transport / neuron projection development / presynapse / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rab6 from Plasmodium falciparum (PDB code 1D5C) / Resolution: 2.3 Å | ||||||
Authors | Garcia-Saez, I. / Tcherniuk, F. / Kozielski, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: The structure of human neuronal Rab6B in the active and inactive form. Authors: Garcia-Saez, I. / Tcherniuk, S. / Kozielski, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fe4.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fe4.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fe4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/2fe4 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/2fe4 | HTTPS FTP |
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-Related 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: 19793.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6B / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9NRW1, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-NO3 / |
#4: Chemical | ChemComp-GDP / |
#5: 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: 1.85 Å3/Da / Density % sol: 33.65 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M sodium acetate pH 5.0, 0.15M ammonium nitrate, 20%-23% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.6 Å / Num. all: 6408 / Num. obs: 6366 / % possible obs: 91.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.052 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 8.8 / Num. unique all: 984 / Rsym value: 0.07 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: Rab6 from Plasmodium falciparum (PDB code 1D5C) Resolution: 2.3→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.028 /
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