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Yorodumi- PDB-2x36: Structure of the proteolytic domain of the Human Mitochondrial Lo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x36 | ||||||
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Title | Structure of the proteolytic domain of the Human Mitochondrial Lon protease | ||||||
Components | LON PROTEASE HOMOLOG, MITOCHONDRIAL | ||||||
Keywords | HYDROLASE / CATALYTIC DYAD / TRANSIT PEPTIDE / MITOCHONDRIA | ||||||
Function / homology | Function and homology information oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / G-quadruplex DNA binding / endopeptidase La / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid ...oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / G-quadruplex DNA binding / endopeptidase La / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / regulation of peptidyl-tyrosine phosphorylation / insulin receptor substrate binding / chaperone-mediated protein complex assembly / DNA polymerase binding / negative regulation of insulin receptor signaling pathway / mitochondrion organization / proteolysis involved in protein catabolic process / Mitochondrial protein degradation / protein catabolic process / ADP binding / single-stranded DNA binding / cellular response to oxidative stress / sequence-specific DNA binding / single-stranded RNA binding / response to hypoxia / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Garcia, J. / Ondrovicova, G. / Blagova, E. / Levdikov, V.M. / Bauer, J.A. / Kutejova, E. / Wilkinson, A.J. / Wilson, K.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Structure of the Catalytic Domain of the Human Mitochondrial Lon Protease: Proposed Relation of Oligomer Formation and Activity. Authors: Garcia-Nafria, J. / Ondrovicova, G. / Blagova, E. / Levdikov, V.M. / Bauer, J.A. / Suzuki, C.K. / Kutejova, E. / Wilkinson, A.J. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x36.cif.gz | 221.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x36.ent.gz | 179.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x36_validation.pdf.gz | 477.5 KB | Display | wwPDB validaton report |
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Full document | 2x36_full_validation.pdf.gz | 516.9 KB | Display | |
Data in XML | 2x36_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 2x36_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x36 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x36 | HTTPS FTP |
-Related structure data
Related structure data | 1rreS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22425.717 Da / Num. of mol.: 6 / Fragment: PROTEOLYTIC DOMAIN, RESIDUES 753-959 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA II References: UniProt: P36776, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M BIS-TRIS PROPANOL PH 6.5, 0.25 M SODIUM ACETATE, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395, 0.9395 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 30, 2008 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→2.11 Å / Num. obs: 82419 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RRE Resolution: 2→34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.377 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.803 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34 Å
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Refine LS restraints |
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