BMRB Entry 25660
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25660
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Title: NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state
Deposition date: 2015-06-15 Original release date: 2016-12-08
Authors: Moreno-Beltran, Blas; Del Conte, Rebecca; Diaz-Quintana, Antonio; De la Rosa, Miguel; Turano, Paola; Diaz-Moreno, Irene
Citation: Diaz-Moreno, Irene. "NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state" Nat. Struct. Biol. ., .-..
Assembly members:
entity, polymer, 104 residues, 12504.514 Da.
PROTOPORPHYRIN IX CONTAINING FE, non-polymer, 616.487 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):
entity: GDVEKGKKIFIMKCSQCHTV
EKGGKHKTGPNLHGLFGRKT
GQAPGYSXTAANKNKGIIWG
EDTLMEYLENPKKYIPGTKM
IFVGIKKKEERADLIAYLKK
ATNE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 423 |
| 15N chemical shifts | 95 |
| 1H chemical shifts | 745 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity | 1 |
| 2 | PROTOPORPHYRIN IX CONTAINING FE | 2 |
Entities:
Entity 1, entity 104 residues - 12504.514 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 | CMF | 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, PROTOPORPHYRIN IX CONTAINING FE - C34 H32 Fe N4 O4 - 616.487 Da.
| 1 | HEM |
Samples:
sample_1: entity, [U-99% 13C; U-99% 15N], 0.7 mM; P-CARBOXI-METHYL-L-PHENYLALANINE 0.7 mM; PROTOPORPHYRIN IX CONTAINING FE 0.7 mM; phosphate buffer 10 mM; H2O 90%; D2O 10%
sample_2: entity, [U-99% 15N], 0.7 mM; P-CARBOXI-METHYL-L-PHENYLALANINE 0.7 mM; PROTOPORPHYRIN IX CONTAINING FE 0.7 mM; phosphate buffer 10 mM; H2O 90%; D2O 10%
sample_3: entity 0.6 mM; P-CARBOXI-METHYL-L-PHENYLALANINE 0.6 mM; PROTOPORPHYRIN IX CONTAINING FE 0.6 mM; phosphate buffer 10 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.05 M; pH: 6.3; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(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 HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
TOPSPIN, Bruker Biospin - collection, processing
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
CARA, Keller and Wuthrich - chemical shift assignment, chemical shift calculation, data analysis, peak picking
XEASY, Bartels et al. - chemical shift assignment, chemical shift calculation, data analysis, peak picking, processing
NMR spectrometers:
- Bruker Avance 950 MHz
- Bruker Avance 700 MHz
- Bruker Avance 500 MHz
- Bruker Avance 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts