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Yorodumi- PDB-3bcc: STIGMATELLIN AND ANTIMYCIN BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bcc | ||||||
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Title | STIGMATELLIN AND ANTIMYCIN BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN | ||||||
Components | (UBIQUINOL CYTOCHROME C ...) x 10 | ||||||
Keywords | OXIDOREDUCTASE / UBIQUINONE / REDOX ENZYME / MEMBRANE PROTEIN / RESPIRATORY CHAIN / STIGMATELLIN / ANTIMYCIN / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information Respiratory electron transport / Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / : / respiratory electron transport chain / metalloendopeptidase activity ...Respiratory electron transport / Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / : / respiratory electron transport chain / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT USING NATIVE STRUCTURE SOLVED BY THE SAME AUTHOR / Resolution: 3.7 Å | ||||||
Authors | Zhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.-I. / Kim, K.K. / Hung, L.-W. / Crofts, A.R. / Berry, E.A. / Kim, S.-H. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Electron transfer by domain movement in cytochrome bc1. Authors: Zhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bcc.cif.gz | 399.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bcc.ent.gz | 319.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bcc_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 3bcc_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3bcc_validation.xml.gz | 95.4 KB | Display | |
Data in CIF | 3bcc_validation.cif.gz | 125.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/3bcc ftp://data.pdbj.org/pub/pdb/validation_reports/bc/3bcc | HTTPS FTP |
-Related structure data
Related structure data | 1bccSC 2bccC 3h1hC 3h1iC 3h1jC 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-UBIQUINOL CYTOCHROME C ... , 10 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 49795.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P31800, quinol-cytochrome-c reductase |
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#2: Protein | Mass: 45091.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P23004, quinol-cytochrome-c reductase |
#3: Protein | Mass: 42622.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P18946, quinol-cytochrome-c reductase |
#4: Protein | Mass: 27357.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P00125, quinol-cytochrome-c reductase |
#5: Protein | Mass: 21739.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase |
#6: Protein | Mass: 13400.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P00129, quinol-cytochrome-c reductase |
#7: Protein | Mass: 9715.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P13271, quinol-cytochrome-c reductase |
#8: Protein | Mass: 9223.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P00126, quinol-cytochrome-c reductase |
#9: Protein/peptide | Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: quinol-cytochrome-c reductase |
#10: Protein | Mass: 7175.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HEART MUSCLE TISSUE / Source: (natural) Gallus gallus (chicken) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00130 |
-Non-polymers , 4 types, 6 molecules
#11: Chemical | #12: Chemical | ChemComp-SIG / | #13: Chemical | ChemComp-AMY / | #14: Chemical | ChemComp-FES / | |
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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: 3.82 Å3/Da / Density % sol: 67.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 Details: 20MM KMES PH6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000, INHIBITOR WAS ADDED FROM ETHANOLIC SOLUTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 29, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 3.5 Å / Num. obs: 80888 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 1.38 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.383 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT USING NATIVE STRUCTURE SOLVED BY THE SAME AUTHOR Starting model: PDB ENTRY 1BCC Resolution: 3.7→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6756288.59 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.201 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.7→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.7→3.92 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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