+Open data
-Basic information
Entry | Database: PDB / ID: 2fv8 | ||||||
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Title | The crystal structure of RhoB in the GDP-bound state | ||||||
Components | Rho-related GTP-binding protein RhoB | ||||||
Keywords | SIGNALING PROTEIN / RHOB / GDP/GTP binding / GTP hydrolysis / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / mitotic cytokinesis ...RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / mitotic cytokinesis / Rho protein signal transduction / negative regulation of cell cycle / regulation of cell migration / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of cell migration / positive regulation of endothelial cell migration / actin filament organization / RHO GTPases Activate Formins / cellular response to ionizing radiation / intracellular protein transport / Schaffer collateral - CA1 synapse / cellular response to hydrogen peroxide / GDP binding / positive regulation of angiogenesis / G alpha (12/13) signalling events / late endosome membrane / angiogenesis / cell differentiation / early endosome / endosome membrane / cell adhesion / positive regulation of apoptotic process / focal adhesion / GTPase activity / apoptotic process / GTP binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Turnbull, A.P. / Soundararajan, M. / Smee, C. / Johansson, C. / Schoch, G. / Gorrec, F. / Bray, J. / Papagrigoriou, E. / von Delft, F. / Weigelt, J. ...Turnbull, A.P. / Soundararajan, M. / Smee, C. / Johansson, C. / Schoch, G. / Gorrec, F. / Bray, J. / Papagrigoriou, E. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of RhoB in the GDP-bound state Authors: Turnbull, A.P. / Soundararajan, M. / Smee, C. / Johansson, C. / Schoch, G. / Gorrec, F. / Bray, J. / Papagrigoriou, E. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fv8.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fv8.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/2fv8 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/2fv8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23632.775 Da / Num. of mol.: 1 / Fragment: residues 4-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOB, ARH6, ARHB / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: P62745 |
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#2: Chemical | ChemComp-GDP / |
#3: 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: 2.08 Å3/Da / Density % sol: 40.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 30 % PEG 3350, 0.075M ammonium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 14890 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Swissmodel Resolution: 1.9→34.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.437 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.163 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 47.9339 Å / Origin y: 37.095 Å / Origin z: 8.3375 Å
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Refinement TLS group |
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