- PDB-2hv4: NMR solution structure refinement of yeast iso-1-ferrocytochrome c -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2hv4
Title
NMR solution structure refinement of yeast iso-1-ferrocytochrome c
Components
Cytochrome c iso-1
Keywords
ELECTRON TRANSPORT / Heme protein
Function / homology
Function and homology information
Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function
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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
1
2D TOCSY
1
3
2
3D 15N-separated NOESY
1
4
2
HNHA
1
5
3
3D 13C-separated NOESY
NMR details
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 ...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-ID
Contents
Solvent system
1
2-3 mM cytochrome c, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O
90% H2O/10% D2O
2
2-3 mM cytochrome c U-15N, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O
90% H2O/10% D2O
3
2-3 mM cytochrome c U-15N,13C, 50 mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O
90% H2O/10% D2O
Sample conditions
Ionic strength: 50 mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 303 K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
700
1
Bruker AVANCE
Bruker
AVANCE
800
2
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
3.1
Bruker
dataanalysis
DYANA
1.5
Guentert
structuresolution
Amber
8
refinement
Refinement
Method: simulated annealing in torsion angle space, restrained energy minimization Software ordinal: 1
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 35
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