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Yorodumi- PDB-6haw: Crystal structure of bovine cytochrome bc1 in complex with 2-pyra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6haw | |||||||||
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Title | Crystal structure of bovine cytochrome bc1 in complex with 2-pyrazolyl quinolone inhibitor WDH2G7 | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / cytochrome bc1 / malaria | |||||||||
Function / homology | Function and homology information mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain ...mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.45 Å | |||||||||
Authors | Amporndanai, K. / Hong, W.D. / O'Neill, P.M. / Hasnain, S.S. / Antonyuk, S.V. | |||||||||
Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Potent Antimalarial 2-Pyrazolyl Quinolonebc1(Qi) Inhibitors with Improved Drug-like Properties. Authors: David Hong, W. / Leung, S.C. / Amporndanai, K. / Davies, J. / Priestley, R.S. / Nixon, G.L. / Berry, N.G. / Samar Hasnain, S. / Antonyuk, S. / Ward, S.A. / Biagini, G.A. / O'Neill, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6haw.cif.gz | 844.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6haw.ent.gz | 682.7 KB | Display | PDB format |
PDBx/mmJSON format | 6haw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6haw ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6haw | HTTPS FTP |
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-Related structure data
Related structure data | 5okdS 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
-Cytochrome b-c1 complex subunit ... , 8 types, 8 molecules ABEFGHIJ
#1: Protein | Mass: 48323.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800 |
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#2: Protein | Mass: 44067.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004 |
#5: Protein | Mass: 21640.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase |
#6: Protein | Mass: 12357.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129 |
#7: Protein | Mass: 8799.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271 |
#8: Protein | Mass: 7515.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126 |
#9: Protein/peptide | Mass: 4827.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase |
#10: Protein | Mass: 6866.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130 |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 42489.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00157 |
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#4: Protein | Mass: 27107.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125 |
-Sugars , 1 types, 1 molecules
#18: Sugar | ChemComp-LMT / |
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-Non-polymers , 13 types, 61 molecules
#11: Chemical | ChemComp-6PE / | ||||||||||||||||||||||
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#12: Chemical | ChemComp-PGE / #13: Chemical | ChemComp-PO4 / #14: Chemical | ChemComp-CDL / #15: Chemical | ChemComp-PG4 / | #16: Chemical | #17: Chemical | #19: Chemical | #20: Chemical | ChemComp-FX2 / | #21: Chemical | ChemComp-HEC / | #22: Chemical | ChemComp-FES / | #23: Chemical | ChemComp-PX4 / | #24: 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: 5.06 Å3/Da / Density % sol: 75.7 % / Description: Bipyramidal red crystal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Protein 40mg/mL with 1.6% HECAMEG; reservoir solution 50mM KPi pH 6.8, 100mM NaCl, 3mM NaN3, 10-12% PEG4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2017 / Details: mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→92.1 Å / Num. obs: 54895 / % possible obs: 90.2 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.074 / Rrim(I) all: 0.179 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3.45→3.55 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 557989 / CC1/2: 0.315 / Rpim(I) all: 0.534 / Rrim(I) all: 1.253 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Starting model: 5OKD Resolution: 3.45→92.1 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.805 / SU B: 56.891 / SU ML: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.49 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 246.77 Å2 / Biso mean: 102.24 Å2 / Biso min: 56.02 Å2
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Refinement step | Cycle: final / Resolution: 3.45→92.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.45→3.54 Å / Rfactor Rfree error: 0 / 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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