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Yorodumi- PDB-1rie: STRUCTURE OF A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR P... -
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-Basic information
Entry | Database: PDB / ID: 1rie | ||||||
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Title | STRUCTURE OF A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR PROTEIN OF THE BOVINE HEART MITOCHONDRIAL CYTOCHROME BC1-COMPLEX | ||||||
Components | RIESKE IRON-SULFUR PROTEIN | ||||||
Keywords | ELECTRON TRANSPORT / OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / HISTIDINE LIGANDS / RIESKE IRON-SULFUR CLUSTER | ||||||
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 / mitochondrial electron transport, ubiquinol to cytochrome c / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity ...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 / mitochondrial electron transport, ubiquinol to cytochrome c / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Iwata, S. / Saynovits, M. / Link, T.A. / Michel, H. | ||||||
Citation | Journal: Structure / Year: 1996 Title: Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution. Authors: Iwata, S. / Saynovits, M. / Link, T.A. / Michel, H. #1: Journal: Eur.J.Biochem. / Year: 1996 Title: Isolation, Characterisation and Crystallisation of a Water-Soluble Fragment of the Rieske Iron-Sulfur Protein of Bovine Heart Mitochondrial Bc1 Complex Authors: Link, T.A. / Saynovits, M. / Assmann, C. / Iwata, S. / Ohnishi, T. / Von Jagow, G. #2: Journal: J.Biol.Chem. / Year: 1993 Title: The Mitochondrial Targeting Presequence of the Rieske Iron-Sulfur Protein is Processed in a Single Step After Insertion Into the Cytochrome Bc1 Complex in Mammals and Retained as a Subunit in the Complex Authors: Brandt, U. / Yu, L. / Yu, C.A. / Trumpower, B.L. #3: Journal: Biochem.Biophys.Res.Commun. / Year: 1990 Title: Cloning and Sequencing of a Cdna Encoding the Rieske Iron-Sulfur Protein of Bovine Heart Mitochondrial Ubiquinol-Cytochrome C Reductase Authors: Usui, S. / Yu, L. / Yu, C.A. #4: Journal: FEBS Lett. / Year: 1987 Title: Isolation and Amino Acid Sequence of the 'Rieske' Iron Sulfur Protein of Beef Heart Ubiquinol:Cytochrome C Reductase Authors: Schagger, H. / Borchart, U. / Machleidt, W. / Link, T.A. / Von Jagow, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 1rie.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rie.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1rie ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1rie | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14440.658 Da / Num. of mol.: 1 / Fragment: SOLUBLE FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P13272, quinol-cytochrome-c reductase |
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#2: Chemical | ChemComp-FES / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 10, 1995 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 18058 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 3.52 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.5 / % possible all: 68 |
Reflection | *PLUS Num. measured all: 63633 |
Reflection shell | *PLUS % possible obs: 68 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 9.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 15880 / Rfactor all: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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