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Open data
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Basic information
Entry | Database: PDB / ID: 5kut | ||||||
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Title | hMiro2 C-terminal GTPase domain, GDP-bound | ||||||
![]() | Mitochondrial Rho GTPase 2 | ||||||
![]() | HYDROLASE / Miro / GTPase / Parkin / Mitochondria | ||||||
Function / homology | ![]() : / : / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / regulation of small GTPase mediated signal transduction / mitochondrion transport along microtubule / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane ...: / : / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / regulation of small GTPase mediated signal transduction / mitochondrion transport along microtubule / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / GTPase activity / calcium ion binding / GTP binding / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klosowiak, J.L. / Focia, P.J. / Rice, S.E. / Freymann, D.M. | ||||||
![]() | ![]() Title: Structural insights into Parkin substrate lysine targeting from minimal Miro substrates. Authors: Klosowiak, J.L. / Park, S. / Smith, K.P. / French, M.E. / Focia, P.J. / Freymann, D.M. / Rice, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 94 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ksoC ![]() 5kspC ![]() 5ksyC ![]() 5kszC ![]() 5ktyC ![]() 5ku1C ![]() 4c0lS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20256.082 Da / Num. of mol.: 3 / Fragment: C-terminal GTPase domain (UNP residues 409-588) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8IXI1, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 14 mg/mL protein, 0.2 M magnesium formate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→52.8 Å / Num. obs: 57061 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.1 |
Reflection shell | Highest resolution: 1.69 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4C0L Resolution: 1.693→37.576 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.693→37.576 Å
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Refine LS restraints |
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LS refinement shell |
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