BMRB Entry 16674
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16674
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Citation: Paixao, Vitor; Vis, Hans; Turner, David. "Redox linked conformational changes in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774." Biochemistry 49, 9620-9629 (2010).
PubMed: 20886839
Assembly members:
cytochrome_c3, polymer, 107 residues, 11383.284 Da.
HEM, non-polymer, 616.487 Da.
Natural source: Common Name: Desulfovibrio desulfuricans Taxonomy ID: 876 Superkingdom: Bacteria Kingdom: not available Genus/species: Desulfovibrio desulfuricans
Experimental source: Production method: purified from the natural source Host organism: Desulfovibrio desulfuricans Vector: na
Entity Sequences (FASTA):
cytochrome_c3: APAVPDKPVEVKGSQKTVMF
PHAPHEKVECVTCHHLVDGK
ESYAKCGSSGCHDDLTAKKG
EKSLYYVVHARGELKHTSCL
ACHSKVVAEKPELKKDLTGC
AKSKCHP
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 1H chemical shifts | 634 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | cytochrome c3 | 1 |
| 2 | HEM 1 | 2 |
| 3 | HEM 2 | 2 |
| 4 | HEM 3 | 2 |
| 5 | HEM 4 | 2 |
Entities:
Entity 1, cytochrome c3 107 residues - 11383.284 Da.
| 1 | ALA | PRO | ALA | VAL | PRO | ASP | LYS | PRO | VAL | GLU | ||||
| 2 | VAL | LYS | GLY | SER | GLN | LYS | THR | VAL | MET | PHE | ||||
| 3 | PRO | HIS | ALA | PRO | HIS | GLU | LYS | VAL | GLU | CYS | ||||
| 4 | VAL | THR | CYS | HIS | HIS | LEU | VAL | ASP | GLY | LYS | ||||
| 5 | GLU | SER | TYR | ALA | LYS | CYS | GLY | SER | SER | GLY | ||||
| 6 | CYS | HIS | ASP | ASP | LEU | THR | ALA | LYS | LYS | GLY | ||||
| 7 | GLU | LYS | SER | LEU | TYR | TYR | VAL | VAL | HIS | ALA | ||||
| 8 | ARG | GLY | GLU | LEU | LYS | HIS | THR | SER | CYS | LEU | ||||
| 9 | ALA | CYS | HIS | SER | LYS | VAL | VAL | ALA | GLU | LYS | ||||
| 10 | PRO | GLU | LEU | LYS | LYS | ASP | LEU | THR | GLY | CYS | ||||
| 11 | ALA | LYS | SER | LYS | CYS | HIS | PRO |
Entity 2, HEM 1 - C34 H32 Fe N4 O4 - 616.487 Da.
| 1 | HEM |
Samples:
sample_1: cytochrome c31.85 – 2.0 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.1 M; pH: 6.46; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
xwinnmr, Bruker Biospin - data analysis, processing
TOPSPIN, Bruker Biospin - data analysis, processing
XEASY, Bartels et al. - chemical shift assignment, peak picking
PARADYANA, (INDYANA) Turner et al. - refinement, structure solution
SPARKY, Goddard - chemical shift assignment, peak picking
Molmol, Koradi, Billeter and Wuthrich - rms and mean structure calculations, superimposition, visual inspection
NMR spectrometers:
- Bruker DRX 500 MHz
- Bruker Avance 800 MHz