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- PDB-2hv4: NMR solution structure refinement of yeast iso-1-ferrocytochrome c -

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Basic information

Entry
Database: PDB / ID: 2hv4
TitleNMR solution structure refinement of yeast iso-1-ferrocytochrome c
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / Heme protein
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / 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
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing in torsion angle space, restrained energy minimization
AuthorsAssfalg, M. / Bertini, I. / Del Conte, R. / 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.
History
DepositionJul 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)12,6902
Polymers12,0721
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 500target function
RepresentativeModel #1fewest violations

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Components

#1: Protein 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 (brewer's yeast)
Gene: CYC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
142HNHA
1533D 13C-separated NOESY
NMR detailsText: The present structure is a refinement of 1YFC obtained through heteronuclear nmr experiments at higher magnetic field, and additional structural constraints. Resonances assignment was based on ...Text: The present structure is a refinement of 1YFC obtained through heteronuclear nmr experiments at higher magnetic field, and additional structural constraints. Resonances assignment was based on HNCA, HN(CO)CA, (H)CCH-TOCSY, H(C)CH-TOCSY, CBCA(CO)NH, and CCC(CO)NH experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
12-3 mM cytochrome c, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
22-3 mM cytochrome c U-15N, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
32-3 mM cytochrome c U-15N,13C, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerdata analysis
DYANA1.5Guentertstructure solution
Amber8refinement
RefinementMethod: simulated annealing in torsion angle space, restrained energy minimization
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 35

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