+Open data
-Basic information
Entry | Database: PDB / ID: 2b6h | ||||||
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Title | Structure of human ADP-ribosylation factor 5 | ||||||
Components | ADP-ribosylation factor 5ADP ribosylation factor | ||||||
Keywords | PROTEIN TRANSPORT / MEMBRANE TRAFFICKING / GDP / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.764 Å | ||||||
Authors | Tempel, W. / Atanassova, A. / Sundarajan, E. / Dimov, S. / Shehab, I. / Lew, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. ...Tempel, W. / Atanassova, A. / Sundarajan, E. / Dimov, S. / Shehab, I. / Lew, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Structure of human ADP-ribosylation factor 5 Authors: Atanassova, A. / Tempel, W. / Sundarajan, E. / Dimov, S. / Shehab, I. / Lew, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b6h.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b6h.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 2b6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/2b6h ftp://data.pdbj.org/pub/pdb/validation_reports/b6/2b6h | HTTPS FTP |
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-Related structure data
Related structure data | 1z6xS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21927.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF5 / Plasmid: p28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P84085 |
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-Non-polymers , 5 types, 108 molecules
#2: Chemical | ChemComp-CL / | ||
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#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-GDP / | ||
#5: Chemical | ChemComp-UNX / #6: 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: 2.9 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, 3% 6-aminocaproic acid, pH 4.6, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 14, 2005 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.76→50 Å / Num. obs: 22373 / % possible obs: 98.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 / Χ2: 1.026 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z6X Resolution: 1.764→32.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.228 / SU B: 2.116 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.764→32.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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