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- PDB-2orl: Solution structure of the cytochrome c- para-aminophenol adduct -

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Basic information

Entry
Database: PDB / ID: 2orl
TitleSolution structure of the cytochrome c- para-aminophenol adduct
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / protein-ligand adduct
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / Respiratory electron transport / Release of apoptotic factors from the mitochondria / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding
Cytochrome c, class IA/ IB / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cytochrome c / Cytochrome c family profile.
Cytochrome c iso-1
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodSOLUTION NMR / combined docking, simulated annealing with NMR restraints
AuthorsAssfalg, M. / Bertini, I. / Del Conte, R. / Giachetti, A. / Turano, P.
CitationJournal: Biochemistry / Year: 2007
Title: Cytochrome c and organic molecules: solution structure of the p-aminophenol adduct.
Authors: Assfalg, M. / Bertini, I. / Del Conte, R. / Giachetti, A. / Turano, P.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7993
Polymers12,0721
Non-polymers7282
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structure with the lowest interaction energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cytochrome c iso-1


Mass: 12071.796 Da / Num. of mol.: 1 / Mutation: C102T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: CYC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Heme C
#3: Chemical ChemComp-4NL / 4-AMINOPHENOL


Mass: 109.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO / 4-Aminophenol

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-separated NOESY

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Sample preparation

DetailsContents: 2-3mM Cytochrome c U-15N, 50mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM phosphate buffer / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameVersionClassification
Topspin1.xcollection
Caradata analysis
Autodockstructure solution
XPLOR-NIHrefinement
RefinementMethod: combined docking, simulated annealing with NMR restraints
Software ordinal: 1
Details: four intermolecular NOEs were used together with intra-protein NOEs and angle constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structure with the lowest interaction energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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