+Open data
-Basic information
Entry | Database: PDB / ID: 5kty | ||||||
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Title | hMiro EF hand and cGTPase domains, GDP and Ca2+ bound state | ||||||
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: 2.522 Å | ||||||
Authors | Klosowiak, J.L. / Focia, P.J. / Rice, S.E. / Freymann, D.M. | ||||||
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 | 5kty.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kty.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kty_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5kty_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5kty_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5kty_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/5kty ftp://data.pdbj.org/pub/pdb/validation_reports/kt/5kty | HTTPS FTP |
-Related structure data
Related structure data | 5ksoC 5kspC 5ksyC 5kszC 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: 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.) 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 | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: 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: 3.11 Å3/Da / Density % sol: 60.39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL protein, 5 mM calcium chloride, 1 mM GDP, 0.04 M potassium phosphate, 16% w/v PEG8000, 20% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å |
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: 21762 / % possible obs: 97.3 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.6 |
Reflection shell | Highest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4C0L Resolution: 2.522→29.174 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.522→29.174 Å
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Refine LS restraints |
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LS refinement shell |
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