BMRB Entry 16096
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16096
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Title: SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G.
Deposition date: 2008-12-29 Original release date: 2009-05-07
Authors: Aramini, James; Rossi, Paolo; Lee, Hsiau-Wei; Alexander, Lemak; Wang, Huang; Foote, Erica; Jiang, Mei; Xiao, Rong; Nair, Rajesh; Swapna, G.; Acton, Thomas; Rost, Burkhard; Everett, John; Montelione, Gaetano
Citation: Aramini, James; Rossi, Paolo; Lee, Hsiau-Wei; Alexander, Lemak; Wang, Huang; Foote, Erica; Jiang, Mei; Xiao, Rong; Nair, Rajesh; Swapna, G.; Acton, Thomas; Rost, Burkhard; Everett, John; Montelione, Gaetano. "SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G." Not known ., .-..
Assembly members:
DvR115G, polymer, 94 residues, 10375.994 Da.
Natural source: Common Name: Desulfovibrio vulgaris Taxonomy ID: 881 Superkingdom: Bacteria Kingdom: not available Genus/species: Desulfovibrio vulgaris
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
DvR115G: MATPQDKLHTVRLFGTVAAD
GLTMLDGAPGVRFRLEDKDN
TSKTVWVLYKGAVPDTFKPG
VEVIIEGGLAPGEDTFKART
LMTKCPLEHHHHHH
- assigned_chemical_shifts
- RDCs
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 392 |
| 15N chemical shifts | 87 |
| 1H chemical shifts | 618 |
| residual dipolar couplings | 49 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DvR115G | 1 |
Entities:
Entity 1, DvR115G 94 residues - 10375.994 Da.
The N-terminal Met and C-terminal affinity tag (LEHHHHHH) are cloning artefacts.
| 1 | MET | ALA | THR | PRO | GLN | ASP | LYS | LEU | HIS | THR | ||||
| 2 | VAL | ARG | LEU | PHE | GLY | THR | VAL | ALA | ALA | ASP | ||||
| 3 | GLY | LEU | THR | MET | LEU | ASP | GLY | ALA | PRO | GLY | ||||
| 4 | VAL | ARG | PHE | ARG | LEU | GLU | ASP | LYS | ASP | ASN | ||||
| 5 | THR | SER | LYS | THR | VAL | TRP | VAL | LEU | TYR | LYS | ||||
| 6 | GLY | ALA | VAL | PRO | ASP | THR | PHE | LYS | PRO | GLY | ||||
| 7 | VAL | GLU | VAL | ILE | ILE | GLU | GLY | GLY | LEU | ALA | ||||
| 8 | PRO | GLY | GLU | ASP | THR | PHE | LYS | ALA | ARG | THR | ||||
| 9 | LEU | MET | THR | LYS | CYS | PRO | LEU | GLU | HIS | HIS | ||||
| 10 | HIS | HIS | HIS | HIS |
Samples:
sample_1: DvR115G, [U-100% 13C; U-100% 15N], 1.3 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM
sample_2: DvR115G, [U-5% 13C; U-100% 15N], 0.56 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM
sample_3: DvR115G, [U-5% 13C; U-100% 15N], 70 %v/v; PEG/hexanol 4.2%
sample_conditions_1: ionic strength: 0.2 M; pH: 4.5; 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 |
| 2D 1H-13C HSQC high res. (L/V methyl stereoassignment) | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | 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 HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N hetNOE | sample_1 | isotropic | sample_conditions_1 |
| 1D 1H-15N T1 and T2 | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N TROSY (for N-H RDCs) | sample_3 | anisotropic | sample_conditions_1 |
Software:
TOPSPIN v2.1, Bruker Biospin - N15 T1/T2 data analysis, collection
VNMRJ v2.1B, Varian - collection
NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.112, Goddard - data analysis, peak picking
PINE, 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 v1.1, 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
PDBStat v5.1, Tejero and Montelione - PDB coordinate analysis
PALES, Zweckstetter and Bax - Prediction of molecular alignment
NMR spectrometers:
- Bruker Avance 800 MHz
- Varian INOVA 600 MHz
- Bruker Avance 600 MHz
Related Database Links:
| PDB |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts