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Open data
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Basic information
Entry | Database: PDB / ID: 1ppj | ||||||||||||
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Title | Bovine cytochrome bc1 complex with stigmatellin and antimycin | ||||||||||||
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![]() | OXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEASE / MPP UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / STIGMATELLIN / ANTIMYCIN | ||||||||||||
Function / homology | ![]() Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / : / respiratory electron transport chain / mitochondrial membrane ...Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / : / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A. | ||||||||||||
![]() | ![]() Title: Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern. Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 855.1 KB | Display | ![]() |
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PDB format | ![]() | 679.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pp9C ![]() 2a06C ![]() 1be3S ![]() 2bccS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.601077, 0.24814, 0.759692), Vector: |
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Components
-Ubiquinol-cytochrome C reductase complex ... , 6 types, 12 molecules ANBOFSGTHUJW
#1: Protein | Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 2 types, 4 molecules CPDQ
#3: Protein | Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Ubiquinol-cytochrome C reductase iron-sulfur subunit, ... , 2 types, 4 molecules ERIV
#5: Protein | Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 7920.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 9 molecules ![](data/chem/img/JZR.gif)
#11: Sugar | ChemComp-JZR / |
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-Non-polymers , 11 types, 1406 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/AZI.gif)
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![](data/chem/img/SMA.gif)
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![](data/chem/img/HEC.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SMA.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/ANY.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#12: Chemical | ChemComp-PO4 / #13: Chemical | ChemComp-AZI / #14: Chemical | ChemComp-GOL / #15: Chemical | ChemComp-HEM / #16: Chemical | #17: Chemical | ChemComp-PEE / #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-CDL / #21: Chemical | #22: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 54.7 % / Description: IRON-SULFUR PROTEINS, HEME PROTEINS |
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Crystal grow | Temperature: 277 K / pH: 6.7 Details: PEG-3350, JEFFAMINE, GLYCEROL, CACODYLATE, HEXYLGLUCOSIDE , pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.70 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→250 Å / Num. obs: 285923 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.63 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 18.689 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 2.819 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1BE3 2BCC Resolution: 2.1→93.53 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5660254.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: A NUMBER OF DIFFERENT DATASETS WERE USED IN THE STRUCTURE DETERMINATION IN ADDITION TO THE DATASET USED FOR THE FINAL REFINEMENT PRESENTED HERE. THE ORIGINAL MOLECULAR REPLACEMENT WAS ...Details: A NUMBER OF DIFFERENT DATASETS WERE USED IN THE STRUCTURE DETERMINATION IN ADDITION TO THE DATASET USED FOR THE FINAL REFINEMENT PRESENTED HERE. THE ORIGINAL MOLECULAR REPLACEMENT WAS CARRIED OUT WITH A LOWER RESOLUTION DATASET. DUE TO LARGE VARIATIONS IN THE CELL PARAMETERS, EACH NEW DATASET WAS RE-SOLVED BY MOLECULAR REPLACEMENT USING A PREVIOUS MODEL. THE SAME R-FREE SET WAS USED IN ALL CASES. STRONG NCS RESTRAINTS WERE USED IN POSITIONAL REFINEMENT. THE COMPLEX WAS DIVIDED INTO 49 TWO-FOLD NCS GROUPS. SPECIFIC RESIDUES NOT OBEYING NCS WERE IDENTIFIED AND RELEASED FROM THE CONSTRAINT. NO NCS RESTRAINT ON B-FACTOR WAS USED. After refinement to convergence against the working set of reflections, the R- and R-Free values of 0.224 and 0.260 were obtained. A final round of positional minimization and restrained B-factor refinement was carried out with identical parameters but against all the data, giving an R-factor of 0.2359. The submitted coordinates are from this final non-cv refinement. Residue (GLU 12 ) and Residue (VAL 17 ) are linked together for chain B and O. Sequence assignment for this fragment is ambiguous. Sequence assignment is also ambiguous for chains I AND V.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.2121 Å2 / ksol: 0.390225 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→93.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 15
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Xplor file |
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