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Open data
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Basic information
Entry | Database: PDB / ID: 5ksy | ||||||
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Title | hMiro1 C-domain GDP Complex P41212 Crystal Form | ||||||
![]() | 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 | ![]() | 46 KB | Display | ![]() |
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PDB format | ![]() | 30.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ksoC ![]() 5kspC ![]() 5kszC ![]() 5ktyC ![]() 5ku1C ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22189.662 Da / Num. of mol.: 1 / Fragment: C-terminal GTPase domain (UNP residues 411-592) 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12 mg/mL protein, 0.1 M Tris, pH 8.5, 16% w/v PEG10000, GDP observed in the structure was carried through from the expression system during purification |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 29, 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: 2.48→51.9 Å / Num. obs: 7933 / % possible obs: 100 % / Redundancy: 25.1 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.1 |
Reflection shell | Highest resolution: 2.48 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4C0L Resolution: 2.482→37.765 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.482→37.765 Å
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Refine LS restraints |
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LS refinement shell |
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