BMRB Entry 18978
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18978
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Title: Solution structure of Ph1500: a homohexameric protein centered on a 12-bladed beta-propeller PubMed: 20961124
Deposition date: 2013-01-28 Original release date: 2013-03-01
Authors: Varnay, Ilka; Truffault, Vincent; Kessler, Horst; Coles, Murray
Citation: Varnay, Ilka; Truffault, Vincent; Djuranovic, Sergej; Ursinus, Astrid; Coles, Murray; Kessler, Horst. "Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric -propeller." J. Am. Chem. Soc. 132, 15692-15698 (2010).
Assembly members:
Ph1500, polymer, 147 residues, 16728.898 Da.
Ph1500N, polymer, 83 residues, 16728.898 Da.
Ph1500C, polymer, 78 residues, 16728.898 Da.
Natural source: Common Name: Euryarchaeotes Taxonomy ID: 53953 Superkingdom: Archaea Kingdom: not available Genus/species: Pyrococcus horikoshii
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Ph1500: EGVIMSELKLKPLPKVELPP
DFVDVIRIKLQGKTVRTGDV
IGISILGKEVKFKVVQAYPS
PLRVEDRTKITLVTHPVDVL
EAKIKGIKDVILDENLIVVI
TEENEVLIFNQNLEELYRGK
FENLNKVLVRNDLVVIIDEQ
KLTLIRT
Ph1500N: MHHHHHHEGVIMSELKLKPL
PKVELPPDFVDVIRIKLQGK
TVRTGDVIGISILGKEVKFK
VVQAYPSPLRVEDRTKITLV
THP
Ph1500C: MHHHHHHVDVLEAKIKGIKD
VILDENLIVVITEENEVLIF
NQNLEELYRGKFENLNKVLV
RNDLVVIIDEQKLTLIRT
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 674 |
| 15N chemical shifts | 131 |
| 1H chemical shifts | 1125 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Ph1500_1 | 1 |
| 2 | Ph1500_2 | 1 |
| 3 | Ph1500_3 | 1 |
| 4 | Ph1500_4 | 1 |
| 5 | Ph1500_5 | 1 |
| 6 | Ph1500_6 | 1 |
| 7 | Ph1500N | 2 |
| 8 | Ph1500C | 3 |
Entities:
Entity 1, Ph1500_1 147 residues - 16728.898 Da.
The first four residues are an artefact of an incorrectly annotated start methionine. Residue numbering refers to the correct start
| 1 | GLU | GLY | VAL | ILE | MET | SER | GLU | LEU | LYS | LEU | ||||
| 2 | LYS | PRO | LEU | PRO | LYS | VAL | GLU | LEU | PRO | PRO | ||||
| 3 | ASP | PHE | VAL | ASP | VAL | ILE | ARG | ILE | LYS | LEU | ||||
| 4 | GLN | GLY | LYS | THR | VAL | ARG | THR | GLY | ASP | VAL | ||||
| 5 | ILE | GLY | ILE | SER | ILE | LEU | GLY | LYS | GLU | VAL | ||||
| 6 | LYS | PHE | LYS | VAL | VAL | GLN | ALA | TYR | PRO | SER | ||||
| 7 | PRO | LEU | ARG | VAL | GLU | ASP | ARG | THR | LYS | ILE | ||||
| 8 | THR | LEU | VAL | THR | HIS | PRO | VAL | ASP | VAL | LEU | ||||
| 9 | GLU | ALA | LYS | ILE | LYS | GLY | ILE | LYS | ASP | VAL | ||||
| 10 | ILE | LEU | ASP | GLU | ASN | LEU | ILE | VAL | VAL | ILE | ||||
| 11 | THR | GLU | GLU | ASN | GLU | VAL | LEU | ILE | PHE | ASN | ||||
| 12 | GLN | ASN | LEU | GLU | GLU | LEU | TYR | ARG | GLY | LYS | ||||
| 13 | PHE | GLU | ASN | LEU | ASN | LYS | VAL | LEU | VAL | ARG | ||||
| 14 | ASN | ASP | LEU | VAL | VAL | ILE | ILE | ASP | GLU | GLN | ||||
| 15 | LYS | LEU | THR | LEU | ILE | ARG | THR |
Entity 2, Ph1500N 83 residues - 16728.898 Da.
The first seven residues are a purification tag. The next four residues are an artefact of an incorrectly annotated start methionine.
| 1 | MET | HIS | HIS | HIS | HIS | HIS | HIS | GLU | GLY | VAL | ||||
| 2 | ILE | MET | SER | GLU | LEU | LYS | LEU | LYS | PRO | LEU | ||||
| 3 | PRO | LYS | VAL | GLU | LEU | PRO | PRO | ASP | PHE | VAL | ||||
| 4 | ASP | VAL | ILE | ARG | ILE | LYS | LEU | GLN | GLY | LYS | ||||
| 5 | THR | VAL | ARG | THR | GLY | ASP | VAL | ILE | GLY | ILE | ||||
| 6 | SER | ILE | LEU | GLY | LYS | GLU | VAL | LYS | PHE | LYS | ||||
| 7 | VAL | VAL | GLN | ALA | TYR | PRO | SER | PRO | LEU | ARG | ||||
| 8 | VAL | GLU | ASP | ARG | THR | LYS | ILE | THR | LEU | VAL | ||||
| 9 | THR | HIS | PRO |
Entity 3, Ph1500C 78 residues - 16728.898 Da.
The first seven residues are a purification tag
| 1 | MET | HIS | HIS | HIS | HIS | HIS | HIS | VAL | ASP | VAL | ||||
| 2 | LEU | GLU | ALA | LYS | ILE | LYS | GLY | ILE | LYS | ASP | ||||
| 3 | VAL | ILE | LEU | ASP | GLU | ASN | LEU | ILE | VAL | VAL | ||||
| 4 | ILE | THR | GLU | GLU | ASN | GLU | VAL | LEU | ILE | PHE | ||||
| 5 | ASN | GLN | ASN | LEU | GLU | GLU | LEU | TYR | ARG | GLY | ||||
| 6 | LYS | PHE | GLU | ASN | LEU | ASN | LYS | VAL | LEU | VAL | ||||
| 7 | ARG | ASN | ASP | LEU | VAL | VAL | ILE | ILE | ASP | GLU | ||||
| 8 | GLN | LYS | LEU | THR | LEU | ILE | ARG | THR |
Samples:
sample_1: Ph1500C, [U-100% 13C; U-100% 15N], 1.2 mM; sodium phosphate 20 mM; sodium chloride 250 mM; H2O 90%; D2O 10%
sample_2: Ph1500C, [U-85% 2H; U-100% 13C; U-100% 15N], 0.6 mM; sodium phosphate 20 mM; sodium chloride 250 mM; H2O 90%; D2O 10%
sample_3: Ph1500N, [U-100% 13C; U-100% 15N], 1.0 mM; sodium phosphate 50 mM; sodium chloride 50 mM; H2O 90%; D2O 10%
sample_4: Ph1500N, [U-100% 15N], 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 90%; D2O 10%
sample_5: Ph1500, [U-85% 2H; U-100% 13C; U-100% 15N], 0.6 mM; sodium phosphate 20 mM; sodium chloride 250 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 300 K
sample_conditions_2: ionic strength: 250 mM; pH: 7.2; pressure: 1 atm; temperature: 353 K
sample_conditions_3: ionic strength: 250 mM; pH: 7.2; pressure: 1 atm; temperature: 318 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCO | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_3 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_4 | isotropic | sample_conditions_1 |
| 3D HNHB | sample_4 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D NNH-NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D CNH-NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D CCH-NOESY | sample_3 | isotropic | sample_conditions_1 |
| 2D 15N-filtered 1H-1H NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D trHNCO | sample_2 | isotropic | sample_conditions_3 |
| 3D trHN(CA)CO | sample_2 | isotropic | sample_conditions_3 |
| 3D trHNCA | sample_2 | isotropic | sample_conditions_3 |
| 3D trHNCACB | sample_2 | isotropic | sample_conditions_3 |
| 3D trHNCO | sample_1 | isotropic | sample_conditions_2 |
| 3D trHNCA | sample_1 | isotropic | sample_conditions_2 |
| 3D trHN(CA)CO | sample_1 | isotropic | sample_conditions_2 |
| 3D HN(CA)HA | sample_1 | isotropic | sample_conditions_2 |
| 3D H(C)CH-TOCSY | sample_1 | isotropic | sample_conditions_2 |
| 3D (H)CCH-COSY | sample_1 | isotropic | sample_conditions_2 |
| 3D (H)CCH-COSY | sample_1 | isotropic | sample_conditions_2 |
| 2D 15N-filtered 1H-1H NOESY | sample_3 | isotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_2 |
| 3D NNH-NOESY | sample_1 | isotropic | sample_conditions_2 |
| 3D CNH-NOESY | sample_1 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_2 |
| 3D CCH-NOESY | sample_1 | isotropic | sample_conditions_2 |
| 2D 1H-15N TROSY | sample_5 | isotropic | sample_conditions_2 |
| 2D 1H-15N CRINEPT | sample_2 | isotropic | sample_conditions_2 |
| 3D HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
Software:
xwinnmr v3.6, Bruker Biospin - collection, processing
SPARKY v3.110, Goddard - data analysis
X-PLOR NIH v2.2.1, Schwieters, Kuszewski, Tjandra and Clore - structure solution
NMR spectrometers:
- Bruker DMX 600 MHz
- Bruker DMX 750 MHz
- Bruker DMX 900 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts