+Open data
-Basic information
Entry | Database: PDB / ID: 5kso | |||||||||
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Title | hMiro1 C-domain GDP-Pi Complex P3121 Crystal Form | |||||||||
Components | Mitochondrial Rho GTPase 1 | |||||||||
Keywords | HYDROLASE / Miro / GTPase / Parkin / Mitochondria | |||||||||
Function / homology | Function and homology information RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / small GTPase-mediated signal transduction / mitochondrion organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / Ub-specific processing proteases ...RHOT1 GTPase cycle / mitochondrial outer membrane permeabilization / cellular homeostasis / regulation of mitochondrion organization / mitochondrion transport along microtubule / small GTPase-mediated signal transduction / mitochondrion 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 / mitochondrion / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Klosowiak, J.L. / Focia, P.J. / Rice, S.E. / Freymann, D.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kso.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kso.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 5kso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kso_validation.pdf.gz | 813.2 KB | Display | wwPDB validaton report |
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Full document | 5kso_full_validation.pdf.gz | 813.5 KB | Display | |
Data in XML | 5kso_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 5kso_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/5kso ftp://data.pdbj.org/pub/pdb/validation_reports/ks/5kso | HTTPS FTP |
-Related structure data
Related structure data | 5kspC 5ksyC 5kszC 5ktyC 5ku1C 5kutC 4c0lS C: citing same article (ref.) 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: 22001.414 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.) Homo sapiens (human) / Gene: RHOT1, ARHT1 / Production host: Escherichia coli (E. coli) 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 | ChemComp-PO4 / |
#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: 2.32 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 19 mg/mL protein, 5 mM magnesium chloride, 0.1 M SPG buffer, pH 5.0, 25% w/v PEG1500, 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97859 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97859 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→82.5 Å / Num. obs: 10140 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 83 |
Reflection shell | Highest resolution: 2.25 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4C0L Resolution: 2.25→33.369 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→33.369 Å
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Refine LS restraints |
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LS refinement shell |
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