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Yorodumi- PDB-3aea: Crystal structure of porcine heart mitochondrial complex II bound... -
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-Basic information
Entry | Database: PDB / ID: 3aea | ||||||
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Title | Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Dimethylaminomethyl-phenyl)-2-trifluoromethyl-benzamide | ||||||
Components |
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Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / respiratory complex II / inhibitors / Electron transport / Iron / Iron-sulfur / Metal-binding / Mitochondrion / Mitochondrion inner membrane / Oxidoreductase / Transit peptide / Transport / Tricarboxylic acid cycle / Heme / Transmembrane / FAD-binding protein / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding ...Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.39 Å | ||||||
Authors | Harada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. ...Harada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. / Inoue, M. / Honma, T. / Tanaka, A. / Kita, K. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2015 Title: Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria Authors: Inaoka, D.K. / Shiba, T. / Sato, D. / Balogun, E.O. / Sasaki, T. / Nagahama, M. / Oda, M. / Matsuoka, S. / Ohmori, J. / Honma, T. / Inoue, M. / Kita, K. / Harada, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aea.cif.gz | 452.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aea.ent.gz | 370.8 KB | Display | PDB format |
PDBx/mmJSON format | 3aea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aea_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3aea_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3aea_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 3aea_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/3aea ftp://data.pdbj.org/pub/pdb/validation_reports/ae/3aea | HTTPS FTP |
-Related structure data
Related structure data | 3abvC 3ae7C 3ae9C 4ysxC 4ysyC 4yszC 4yt0C 4ytmC 4ytpC 4yxdC 5c2tC 1zoyS 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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Unit cell |
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-Components
-Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD
#1: Protein | Mass: 68313.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: Q0QF01, succinate dehydrogenase |
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#2: Protein | Mass: 28764.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: Q007T0, succinate dehydrogenase |
#4: Protein | Mass: 10936.758 Da / Num. of mol.: 1 / Fragment: residues 57-159 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: A5GZW8 |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 15304.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: D0VWV4 |
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-Non-polymers , 8 types, 8 molecules
#5: Chemical | ChemComp-FAD / |
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#6: Chemical | ChemComp-MLI / |
#7: Chemical | ChemComp-FES / |
#8: Chemical | ChemComp-SF4 / |
#9: Chemical | ChemComp-F3S / |
#10: Chemical | ChemComp-HEM / |
#11: Chemical | ChemComp-F9A / |
#12: Chemical | ChemComp-EPH / |
-Details
Compound details | THESE COMPLEX FORMS MITOCHONDRHas protein modification | Y | Sequence details | THE SEQUENCE OF CHAIN D IS REFERRED IN REF 2 IN A5GZW8, UNIPROT. | |
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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: 3.58 Å3/Da / Density % sol: 65.65 % / Mosaicity: 0.368 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 25mM HEPES-NAOH, 5% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.39→50 Å / Num. obs: 25146 / % possible obs: 98.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Χ2: 0.939 / Net I/σ(I): 17.333 |
Reflection shell | Resolution: 3.39→3.51 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 3.18 / Num. unique all: 2338 / Χ2: 1.162 / % possible all: 93.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZOY Resolution: 3.39→43.77 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.773 / SU B: 62.262 / SU ML: 0.494 / SU R Cruickshank DPI: 0.496 / SU Rfree: 0.599 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.599 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 177.54 Å2 / Biso mean: 113.726 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.39→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.386→3.474 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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