BMRB Entry 36338
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36338
MolProbity Validation Chart
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NMR-STAR v3 text file.
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Title: Solution NMR structure of fold-K Mussoc; de novo designed protein with an asymmetric all-alpha topology PubMed: 38177681
Deposition date: 2020-03-25 Original release date: 2022-01-28
Authors: Kobayashi, N.; Nagashima, T.; Sakuma, K.; Kosugi, T.; Koga, R.; Koga, N.
Citation: Sakuma, Koya; Kobayashi, Naohiro; Sugiki, Toshihiko; Nagashima, Toshio; Fujiwara, Toshimichi; Suzuki, Kano; Kobayashi, Naoya; Murata, Takeshi; Kosugi, Takahiro; Tatsumi-Koga, Rie; Koga, Nobuyasu. "Design of complicated all-alpha protein structures" Nat. Struct. Mol. Biol. 31, 275-282 (2024).
Assembly members:
entity_1, polymer, 137 residues, 15536.427 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: GDEDKEKLKREAERALSEAL
SEFEKQGKITPETLKRLAEE
IAEAALAQQQGDSERLEKAA
RRFAETLLRALKESGASAEE
IEEAIERIRKALSKAPSPQL
QKLANSPQWQTALQEAIKKA
RQEKKEKGSLEHHHHHH
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 513 |
15N chemical shifts | 123 |
1H chemical shifts | 792 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 137 residues - 15536.427 Da.
1 | GLY | ASP | GLU | ASP | LYS | GLU | LYS | LEU | LYS | ARG | ||||
2 | GLU | ALA | GLU | ARG | ALA | LEU | SER | GLU | ALA | LEU | ||||
3 | SER | GLU | PHE | GLU | LYS | GLN | GLY | LYS | ILE | THR | ||||
4 | PRO | GLU | THR | LEU | LYS | ARG | LEU | ALA | GLU | GLU | ||||
5 | ILE | ALA | GLU | ALA | ALA | LEU | ALA | GLN | GLN | GLN | ||||
6 | GLY | ASP | SER | GLU | ARG | LEU | GLU | LYS | ALA | ALA | ||||
7 | ARG | ARG | PHE | ALA | GLU | THR | LEU | LEU | ARG | ALA | ||||
8 | LEU | LYS | GLU | SER | GLY | ALA | SER | ALA | GLU | GLU | ||||
9 | ILE | GLU | GLU | ALA | ILE | GLU | ARG | ILE | ARG | LYS | ||||
10 | ALA | LEU | SER | LYS | ALA | PRO | SER | PRO | GLN | LEU | ||||
11 | GLN | LYS | LEU | ALA | ASN | SER | PRO | GLN | TRP | GLN | ||||
12 | THR | ALA | LEU | GLN | GLU | ALA | ILE | LYS | LYS | ALA | ||||
13 | ARG | GLN | GLU | LYS | LYS | GLU | LYS | GLY | SER | LEU | ||||
14 | GLU | HIS | HIS | HIS | HIS | HIS | HIS |
Samples:
sample_1: foldK4, [U-100% 13C; U-100% 15N], 0.5 mM; potassium phosphate 1.06 mM; sodium chloride 155.2 mM; sodium phosphate 2.97 mM; H2O 95%; D2O, [U-2H], 5%
sample_2: foldK4, [U-100% 13C; U-100% 15N], 0.2 mM; Pf1 phage 10.0 mg/mL; potassium phosphate 1.06 mM; sodium chloride 155.2 mM; sodium phosphate 2.97 mM; H2O 95%; D2O, [U-2H], 5%
sample_conditions_1: ionic strength: 160 mM; pH: 7.4; pressure: 1 atm; temperature: 303 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 |
2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
3D HNCO | sample_1 | isotropic | sample_conditions_1 |
3D HCACO | sample_1 | isotropic | sample_conditions_1 |
3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
3D H(NCA)NH | sample_1 | isotropic | sample_conditions_1 |
3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
3D HCCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
2D 1H-15N HSQC IPAP | sample_1 | isotropic | sample_conditions_1 |
2D 1H-15N HSQC IPAP | sample_2 | anisotropic | sample_conditions_1 |
Software:
Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
CYANA v3.98, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure calculation
MAGRO v2.01.34, Kobayashi, N. - peak picking
NMRPipe v2017, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView v9.0, Johnson, One Moon Scientific - data analysis
TALOS v2017, Cornilescu, Delaglio and Bax - data analysis
TopSpin v3.2, Bruker Biospin - collection
qMDD v2.6, Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk - processing
NMR spectrometers:
- Bruker AVANCE III 600 MHz
- Bruker AVANCE III 700 MHz
- Bruker AVANCE III 900 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts