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Yorodumi- PDB-6zfs: Crystal structure of bovine cytochrome bc1 in complex with quinol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zfs | |||||||||
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Title | Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor WDH-1U-4 | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Amporndanai, K. / O'Neill, P.M. / Hong, W.D. / Amewu, R.K. / Pidathala, C. / Berry, N.G. / Biagini, G.A. / Leung, S.C. / Hasnain, S.S. / Antonyuk, S.V. | |||||||||
Citation | Journal: To Be Published Title: Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials Authors: Amporndanai, K. / O'Neill, P.M. / Hong, W.D. / Amewu, R.K. / Pidathala, C. / Berry, N. / Biangini, G.A. / Leung, S.C. / Hasnain, S.S. / Antonyuk, S.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zfs.cif.gz | 841 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zfs.ent.gz | 685.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/6zfs ftp://data.pdbj.org/pub/pdb/validation_reports/zf/6zfs | HTTPS FTP |
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-Related structure data
Related structure data | 6zftC 6zfuC 5okdS S: Starting model for refinement C: citing same article (ref.) |
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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: 49062.031 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: 44730.262 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: 12356.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129 |
#7: Protein | Mass: 8856.277 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, quinol-cytochrome-c reductase |
-Sugars , 1 types, 1 molecules
#15: Sugar | ChemComp-LMT / |
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-Non-polymers , 11 types, 58 molecules
#11: Chemical | ChemComp-6PE / | ||||||||||||||||||
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#12: Chemical | ChemComp-PO4 / #13: Chemical | ChemComp-CDL / #14: Chemical | #16: Chemical | ChemComp-PG4 / | #17: Chemical | #18: Chemical | ChemComp-JGW / | #19: Chemical | ChemComp-HEC / | #20: Chemical | ChemComp-FES / | #21: Chemical | ChemComp-PX4 / | #22: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 4.85 Å3/Da / Density % sol: 74.65 % / 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, 10-13% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2017 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→90.74 Å / Num. obs: 55066 / % possible obs: 97.4 % / Redundancy: 5.4 % / CC1/2: 0.968 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.091 / Rrim(I) all: 0.219 / Net I/σ(I): 7 / Num. measured all: 296628 / Scaling rejects: 211 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OKD Resolution: 3.5→90.74 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.787 / SU B: 60.553 / SU ML: 0.397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 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: 267.95 Å2 / Biso mean: 134.235 Å2 / Biso min: 18.52 Å2
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Refinement step | Cycle: final / Resolution: 3.5→90.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.591 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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