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Yorodumi- PDB-1i6d: SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i6d | ||||||
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Title | SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE | ||||||
Components | CYTOCHROME C552 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME C552 / HEME / REDOX STATES / ISOTOPE ENRICHMENT {13C/15N} / NMR SPECTROSCOPY / SOLUTION STRUCTURE | ||||||
Function / homology | Function and homology information electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, ENERGY MINIMIZATION | ||||||
Authors | Reincke, B. / Perez, C. / Pristovsek, P. / Luecke, C. / Ludwig, C. / Loehr, F. / Rogov, V.V. / Ludwig, B. / Rueterjans, H. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Solution structure and dynamics of the functional domain of Paracoccus denitrificans cytochrome c(552) in both redox states. Authors: Reincke, B. / Perez, C. / Pristovsek, P. / Lucke, C. / Ludwig, C. / Lohr, F. / Rogov, V.V. / Ludwig, B. / Ruterjans, H. #1: Journal: Eur.J.Biochem. / Year: 2000 Title: Solution Structure of the Functional Domain of Paracoccus Denitrificans Cytochrome C552 in the Reduced State Authors: Pristovsek, P. / Luecke, C. / Reincke, B. / Ludwig, B. / Rueterjans, H. #2: Journal: J.Mol.Biol. / Year: 2000 Title: Structure of the Soluble Domain of Cytochrome C552 from Paracoccus Denitrificans in the Oxidized and Reduced States Authors: Harrenga, A. / Reincke, B. / Rueterjans, H. / Ludwig, B. / Michel, H. #3: Journal: Biochim.Biophys.Acta / Year: 1999 Title: Heterologous Expression of Soluble Fragments of Cytochrome C552 Acting as Electron Donor to the Paracoccus Denitrificans Cytochrome C Oxidase Authors: Reincke, B. / Thoeny-Meyer, L. / Dannehl, C. / Odenwald, A. / Aidim, M. / Witt, H. / Rueterjans, H. / Ludwig, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6d.cif.gz | 599.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6d.ent.gz | 515.9 KB | Display | PDB format |
PDBx/mmJSON format | 1i6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6d ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10553.977 Da / Num. of mol.: 1 / Fragment: SOLUBLE FUNCTIONAL DOMAIN Source method: isolated from a genetically manipulated source Details: COVALENT THIOETHER LINKAGES FROM HEME COFACTOR TO BOTH CYS14 AND CYS17 Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1235 / Description: HETEROLOGOUS EXPRESSION / Cellular location: PERIPLASM / Gene: CYCM / Plasmid: PET22B+ / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P54820 |
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#2: Chemical | ChemComp-HEC / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE EXPERIMENTS WERE PERFORMED WITH REDUCED UNLABELED, 15N-LABELED OR 13C-LABELED CYTOCHROME C552. |
-Sample preparation
Details | Contents: 20 MM PHOSPHATE, 90% H2O/ 10% D2O |
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Sample conditions | pH: 5.50 / Temperature: 298.00 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, ENERGY MINIMIZATION / Software ordinal: 1 / Details: ENERGY MINIMIZATION. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20 |