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- PDB-3h1k: Chicken cytochrome BC1 complex with ZN++ and an iodinated derivat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h1k | |||||||||
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Title | Chicken cytochrome BC1 complex with ZN++ and an iodinated derivative of kresoxim-methyl bound | |||||||||
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![]() | OXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / UBIQUINONE / REDOX ENZYME / ZINC / KRESOXIM-METHYL / RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE IRON / MEMBRANE / METAL-BINDING / MITOCHONDRION / TRANSMEMBRANE / Iron / Mitochondrion inner membrane / Transport / Disulfide bond / Iron-sulfur / Transit peptide | |||||||||
Function / homology | ![]() Respiratory electron transport / quinol-cytochrome-c reductase / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / electron transfer activity ...Respiratory electron transport / quinol-cytochrome-c reductase / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / electron transfer activity / oxidoreductase activity / heme binding / mitochondrion / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Berry, E.A. / Zhang, Z. / Bellamy, H.D. / Huang, L.S. | |||||||||
![]() | ![]() Title: Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex Authors: Berry, E.A. / Zhang, Z. / Bellamy, H.D. / Huang, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 834.9 KB | Display | ![]() |
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PDB format | ![]() | 663.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bccS ![]() 2ppj 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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Unit cell |
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Components
-MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO
#1: Protein | Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX31*PLUS, quinol-cytochrome-c reductase #2: Protein | Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX29*PLUS, quinol-cytochrome-c reductase |
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-Protein , 2 types, 4 molecules CPDQ
#3: Protein | Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX26*PLUS, quinol-cytochrome-c reductase |
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-Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules ERIV
#5: Protein | Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: sequence database residues 77-272 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein/peptide | Mass: 4785.649 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-76 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 4 types, 8 molecules FSGTHUJW
#6: Protein | Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX30*PLUS, quinol-cytochrome-c reductase #7: Protein | Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX32*PLUS, quinol-cytochrome-c reductase #8: Protein | Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX28*PLUS, quinol-cytochrome-c reductase #10: Protein | Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D0VX27*PLUS, quinol-cytochrome-c reductase |
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-Sugars , 1 types, 5 molecules ![](data/chem/img/BOG.gif)
#20: Sugar | ChemComp-BOG / |
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-Non-polymers , 11 types, 48 molecules ![](data/chem/img/PEE.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/IKR.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/IKR.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | ChemComp-PEE / #12: Chemical | ChemComp-UNL / Num. of mol.: 5 / Source method: obtained synthetically #13: Chemical | ChemComp-HEM / #14: Chemical | #15: Chemical | #16: Chemical | ChemComp-CDL / #17: Chemical | #18: Chemical | #19: Chemical | #21: Chemical | #22: Water | ChemComp-HOH / | |
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-Details
Sequence details | IN THE COORDINATES THE FIRST 15 RESIDUES IN CHAINS I AND V ARE MODELED AS UNK BECAUSE THE SEQUENCE ...IN THE COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 20MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000. The Kresoxim-methyl derivative WAS ADDED to the protein FROM ETHANOLIC SOLUTION. After verifying good diffraction by these ...Details: 20MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000. The Kresoxim-methyl derivative WAS ADDED to the protein FROM ETHANOLIC SOLUTION. After verifying good diffraction by these crystals, some were transferred to a drop of mother liquor supplemented with glycerol and ~0.2 mM ZnCl2. After 1 week this crystal was flash-cooled for data collection. During analysis of Zn binding presence of the inhibitor was overlooked, and in the primary citation publication the anomalous signal of I in the inhibitor was mistakenly attributed to a second Zn binding site, Zn02. VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 3.48→42.61 Å / Num. all: 87072 / Num. obs: 87072 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 84.8 Å2 / Rsym value: 0.204 / Net I/σ(I): 9.49 |
Reflection shell | Resolution: 3.48→3.55 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.14 / Num. unique all: 3144 / Rsym value: 0.99 / % possible all: 65.2 |
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Processing
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1BCC after further correction/refinement Resolution: 3.48→18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4943137.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.8112 Å2 / ksol: 0.26 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.48→18 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.48→3.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 7
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Xplor file |
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