BMRB Entry 25908
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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/BMR25908
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Title: Solution structure of oxidized human cytochrome c PubMed: 26718409
Deposition date: 2015-11-24 Original release date: 2016-02-15
Authors: Imai, Mizue; Saio, Tomohide; Kumeta, Hiroyuki; Uchida, Takeshi; Inagaki, Fuyuhiko; Ishimori, Koichiro
Citation: Imai, Mizue; Saio, Tomohide; Kumeta, Hiroyuki; Uchida, Takeshi; Inagaki, Fuyuhiko; Ishimori, Koichiro. "Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c" Biochem. Biophys. Res. Commun. 469, 978-984 (2016).
Assembly members:
Cyt_c, polymer, 104 residues, 11640.677 Da.
HEME C, non-polymer, 618.503 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Cyt_c: GDVEKGKKIFIMKCSQCHTV
EKGGKHKTGPNLHGLFGRKT
GQAPGYSYTAANKNKGIIWG
EDTLMEYLENPKKYIPGTKM
IFVGIKKKEERADLIAYLKK
ATNE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 465 |
| 15N chemical shifts | 105 |
| 1H chemical shifts | 774 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Cytochrome c | 1 |
| 2 | HEME C | 2 |
Entities:
Entity 1, Cytochrome c 104 residues - 11640.677 Da.
| 1 | GLY | ASP | VAL | GLU | LYS | GLY | LYS | LYS | ILE | PHE | ||||
| 2 | ILE | MET | LYS | CYS | SER | GLN | CYS | HIS | THR | VAL | ||||
| 3 | GLU | LYS | GLY | GLY | LYS | HIS | LYS | THR | GLY | PRO | ||||
| 4 | ASN | LEU | HIS | GLY | LEU | PHE | GLY | ARG | LYS | THR | ||||
| 5 | GLY | GLN | ALA | PRO | GLY | TYR | SER | TYR | THR | ALA | ||||
| 6 | ALA | ASN | LYS | ASN | LYS | GLY | ILE | ILE | TRP | GLY | ||||
| 7 | GLU | ASP | THR | LEU | MET | GLU | TYR | LEU | GLU | ASN | ||||
| 8 | PRO | LYS | LYS | TYR | ILE | PRO | GLY | THR | LYS | MET | ||||
| 9 | ILE | PHE | VAL | GLY | ILE | LYS | LYS | LYS | GLU | GLU | ||||
| 10 | ARG | ALA | ASP | LEU | ILE | ALA | TYR | LEU | LYS | LYS | ||||
| 11 | ALA | THR | ASN | GLU |
Entity 2, HEME C - C34 H34 Fe N4 O4 - 618.503 Da.
| 1 | HEC |
Samples:
sample_1: Cyt c, [U-99% 13C; U-99% 15N], 0.5 – 1 mM; sodium phosphate 50 mM; H2O 95%; D2O, [U-2H], 5%
sample_conditions_1: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)HA | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aromatic | sample_1 | isotropic | sample_conditions_1 |
| HbCbCgCdHd | sample_1 | isotropic | sample_conditions_1 |
| HbCbCgCdCeHe | sample_1 | isotropic | sample_conditions_1 |
Software:
VNMRJ, Varian - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TALOS+, Yang Shen,Frank Delaglio,Gabriel Cornilescu, Ad bax - data analysis
SPARKY, Goddard - chemical shift assignment, peak picking, refinement
CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution
NMR spectrometers:
- Agilent INOVA 800 MHz
- Agilent INOVA 600 MHz
- Agilent INOVA 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts