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Yorodumi- PDB-2qjk: Crystal Structure Analysis of mutant rhodobacter sphaeroides bc1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qjk | ||||||
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Title | Crystal Structure Analysis of mutant rhodobacter sphaeroides bc1 with stigmatellin and antimycin | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Cytochrome b / TM helices / cytochrome c1 / C-terminal TM helix / iron-sulfur-protein / N-terminal TM / Heme / Membrane / Metal-binding / Respiratory chain / Transmembrane / Transport / 2Fe-2S / Inner membrane / Oxidoreductase | ||||||
Function / homology | Function and homology information respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane ...respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Esser, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Inhibitor-complexed structures of the cytochrome bc1 from the photosynthetic bacterium Rhodobacter sphaeroides. Authors: Esser, L. / Elberry, M. / Zhou, F. / Yu, C.A. / Yu, L. / Xia, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qjk.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2qjk.ent.gz | 857 KB | Display | PDB format |
PDBx/mmJSON format | 2qjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qjk ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qjk | HTTPS FTP |
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-Related structure data
Related structure data | 2qjpC 2qjyC 2fynS 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 3 types, 18 molecules ADGJMPBEHKNQCFILOR
#1: Protein | Mass: 48437.641 Da / Num. of mol.: 6 / Mutation: S287R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petB, fbcB / Plasmid: pRKDfbcFBCQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q02761 #2: Protein | Mass: 27786.162 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: fbcC / Plasmid: pRKDfbcFBCQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IY11, UniProt: Q02760*PLUS #3: Protein | Mass: 19059.439 Da / Num. of mol.: 6 / Mutation: V135S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Plasmid: pRKDfbcFBCQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q02762, quinol-cytochrome-c reductase |
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-Sugars , 1 types, 6 molecules
#4: Sugar | ChemComp-BGL / |
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-Non-polymers , 6 types, 48 molecules
#5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-SMA / #7: Chemical | ChemComp-LOP / ( #8: Chemical | ChemComp-ANJ / ( #9: Chemical | ChemComp-SR / #10: Chemical | ChemComp-FES / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.25 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.35 Details: 7.5% PEG 400, 0.2M NaCl, 0.2M Histidine, 0.1M Bistris, 10 mM Sr(NO3)2, 0.5% betaoctyl glucopyranoside, 0.02% cymal-6, 10% Glycerol, 5 mM NaN3, 1 mM stigmatellin, 1 mM Antimycin , pH 7.35, ...Details: 7.5% PEG 400, 0.2M NaCl, 0.2M Histidine, 0.1M Bistris, 10 mM Sr(NO3)2, 0.5% betaoctyl glucopyranoside, 0.02% cymal-6, 10% Glycerol, 5 mM NaN3, 1 mM stigmatellin, 1 mM Antimycin , pH 7.35, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 21, 2005 / Details: mirrors |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 143931 / Num. obs: 143931 / % possible obs: 99.7 % / Observed criterion σ(I): -1 / Redundancy: 6 % / Biso Wilson estimate: 104 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 9.81 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.07 / Num. unique all: 14141 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FYN Resolution: 3.1→18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4344367.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: 89 NCS restraints
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.0177 Å2 / ksol: 0.275707 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→18 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINT | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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