+Open data
-Basic information
Entry | Database: PDB / ID: 2a5j | ||||||
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Title | Crystal Structure of Human RAB2B | ||||||
Components | Ras-related protein Rab-2B | ||||||
Keywords | PROTEIN TRANSPORT / GTPase / Signal transduction / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information RAB geranylgeranylation / positive regulation of exocytosis / vesicle-mediated transport / protein transport / presynapse / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / Golgi apparatus ...RAB geranylgeranylation / positive regulation of exocytosis / vesicle-mediated transport / protein transport / presynapse / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å | ||||||
Authors | Dong, A. / Wang, J. / Shen, Y. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human RAB2B Authors: Wang, J. / Dong, A. / Shen, Y. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Bochkarev, A. / Park, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a5j.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a5j.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 2a5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/2a5j ftp://data.pdbj.org/pub/pdb/validation_reports/a5/2a5j | HTTPS FTP |
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-Related structure data
Related structure data | 1oivS S: Starting model for refinement |
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Similar 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: 21753.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8WUD1 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: 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: 2.1 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6.5 Details: 30% PEG5000, 02M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.966 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 29, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→24.6 Å / Num. all: 27473 / Num. obs: 27473 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1127 / Rsym value: 0.419 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OIV Resolution: 1.501→24.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.344 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.089 / ESU R Free: 0.088 / 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: 17.043 Å2
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Refinement step | Cycle: LAST / Resolution: 1.501→24.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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