BMRB Entry 16272
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16272
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Title: Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.
Deposition date: 2009-05-03 Original release date: 2010-03-09
Authors: Aramini, James; Belote, Rachel; Ciccosanti, Colleen; Jiang, Mei; Rost, Burkhard; Nair, Rajesh; Swapna, G.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano
Citation: Aramini, James; Belote, Rachel; Ciccosanti, Colleen; Jiang, Mei; Rost, Burkhard; Nair, Rajesh; Swapna, G.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano. "Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247." Not known ., .-..
Assembly members:
VpR247, polymer, 108 residues, 12341.439 Da.
Natural source: Common Name: Vibrio parahaemolyticus Taxonomy ID: 670 Superkingdom: Bacteria Kingdom: not available Genus/species: Vibrio parahaemolyticus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
VpR247: MDQFLVQIFAVIHQIPKGKV
STYGEIAKMAGYPGYARHVG
KALGNLPEGSKLPWFRVINS
QGKISLKGRDLDRQKQKLEA
EGIEVSEIGKIALRKYKWQP
LEHHHHHH
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 486 |
| 15N chemical shifts | 104 |
| 1H chemical shifts | 768 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | VpR247 | 1 |
Entities:
Entity 1, VpR247 108 residues - 12341.439 Da.
| 1 | MET | ASP | GLN | PHE | LEU | VAL | GLN | ILE | PHE | ALA | ||||
| 2 | VAL | ILE | HIS | GLN | ILE | PRO | LYS | GLY | LYS | VAL | ||||
| 3 | SER | THR | TYR | GLY | GLU | ILE | ALA | LYS | MET | ALA | ||||
| 4 | GLY | TYR | PRO | GLY | TYR | ALA | ARG | HIS | VAL | GLY | ||||
| 5 | LYS | ALA | LEU | GLY | ASN | LEU | PRO | GLU | GLY | SER | ||||
| 6 | LYS | LEU | PRO | TRP | PHE | ARG | VAL | ILE | ASN | SER | ||||
| 7 | GLN | GLY | LYS | ILE | SER | LEU | LYS | GLY | ARG | ASP | ||||
| 8 | LEU | ASP | ARG | GLN | LYS | GLN | LYS | LEU | GLU | ALA | ||||
| 9 | GLU | GLY | ILE | GLU | VAL | SER | GLU | ILE | GLY | LYS | ||||
| 10 | ILE | ALA | LEU | ARG | LYS | TYR | LYS | TRP | GLN | PRO | ||||
| 11 | LEU | GLU | HIS | HIS | HIS | HIS | HIS | HIS |
Samples:
sample_1: VpR247, [U-100% 13C; U-100% 15N], 0.94 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H20 90%; D20 10%
sample_2: VpR247, [U-100% 13C; U-100% 15N], 0.94 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H20 90%; D20 10%
sample_3: VpR247, [U-5% 13C; U-100% 15N], 0.92 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H20 90%; D20 10%
sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; pressure: 1.0 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 | sample_1 | isotropic | sample_conditions_1 |
| 3D simultaneous CN NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N hetNOE | sample_2 | isotropic | sample_conditions_1 |
| 1D 1H-15N T1 and T2 | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC high res. (L/V methyl stereoassignment) | sample_3 | isotropic | sample_conditions_1 |
Software:
TOPSPIN v2.1, Bruker Biospin - collection, data analysis
NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.112, Goddard - data analysis, peak picking
PINE v1.0, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment
AutoAssign v2.4.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment, validation
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - RPF analysis
PSVS v1.3, Bhattacharya and Montelione - structure quality analysis
MolProbity v3.15, Richardson - structure quality analysis
PDBStat v5.1, Tejero and Montelione - PDB coordinate analysis
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Related Database Links:
| BMRB | 16283 |
| PDB | |
| DBJ | BAC59214 |
| GB | AGB09412 AGQ90485 AGQ98830 AHI99009 AKU55569 |
| REF | NP_797330 WP_005461131 WP_005481834 WP_021449579 WP_025501692 |
| SP | A6B4U8 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts