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Open data
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Basic information
Entry | Database: PDB / ID: 5ku1 | ||||||
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Title | hMiro1 EF hand and cGTPase domains in the GDP-bound state | ||||||
![]() | Mitochondrial Rho GTPase 1 | ||||||
![]() | HYDROLASE / Miro / GTPase / Parkin / Mitochondria | ||||||
Function / homology | ![]() RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / small GTPase-mediated signal transduction / mitochondrion organization / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane ...RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / small GTPase-mediated signal transduction / mitochondrion organization / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / Ub-specific processing proteases / GTPase activity / calcium ion binding / GTP binding / signal transduction / mitochondrion / membrane 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 | ![]() | 98.6 KB | Display | ![]() |
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PDB format | ![]() | 72.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.5 KB | Display | ![]() |
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Full document | ![]() | 789.1 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ksoC ![]() 5kspC ![]() 5ksyC ![]() 5kszC ![]() 5ktyC ![]() 5kutC ![]() 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
#1: Protein | Mass: 49065.859 Da / Num. of mol.: 1 / Fragment: hand and cGTPase domains (UNP residues 177-592) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8IXI2, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement | ||||
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#2: Chemical | ChemComp-GDP / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 9 mg/mL protein, 5 mM magnesium chloride, 1 mM GDP, 0.2 M ammonium sulfate, 0.1 M trisodium citrate, pH 5.6, 25% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2014 |
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: 2.5→30 Å / Num. obs: 21325 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 30.5 |
Reflection shell | Highest resolution: 2.5 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4C0L Resolution: 2.501→29.806 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→29.806 Å
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Refine LS restraints |
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LS refinement shell |
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