BMRB Entry 15339
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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/BMR15339
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Title: Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus. Northeast Structural Genomics Target VpR55 PubMed: TBA
Deposition date: 2007-06-28 Original release date: 2007-07-27
Authors: Tang, Yuefeng; Rossi, Paolo; Swapna, G.V.T; Wang, Huang; Jiang, Mei; Cunningham, Kellie; Owens, Leah; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano
Citation: Tang, Yuefeng; Rossi, Paolo; Swapna, G.V.T; Wang, Huang; Jiang, Mei; Cunningham, Kellie; Owens, Leah; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano. "Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus" Not known ., .-..
Assembly members:
VpR55, polymer, 65 residues, 7115.986 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):
VpR55: MKRQKRDRLERAQSQGYKAG
LNGRSQEACPYQQVDARSYW
LGGWRDARDEKQSGLYKLEH
HHHHH
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 258 |
| 15N chemical shifts | 71 |
| 1H chemical shifts | 407 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Ribosome Modulation Factor | 1 |
Entities:
Entity 1, Ribosome Modulation Factor 65 residues - 7115.986 Da.
Residue 58-65 represent a non-native affinity purification tag (LEHHHHHH)
| 1 | MET | LYS | ARG | GLN | LYS | ARG | ASP | ARG | LEU | GLU | ||||
| 2 | ARG | ALA | GLN | SER | GLN | GLY | TYR | LYS | ALA | GLY | ||||
| 3 | LEU | ASN | GLY | ARG | SER | GLN | GLU | ALA | CYS | PRO | ||||
| 4 | TYR | GLN | GLN | VAL | ASP | ALA | ARG | SER | TYR | TRP | ||||
| 5 | LEU | GLY | GLY | TRP | ARG | ASP | ALA | ARG | ASP | GLU | ||||
| 6 | LYS | GLN | SER | GLY | LEU | TYR | LYS | LEU | GLU | HIS | ||||
| 7 | HIS | HIS | HIS | HIS | HIS |
Samples:
sample_1: VpR55, [U-100% 13C; U-100% 15N], 1.1 mM; MES 20 mM; NaCl 100 mM; CaCl2 5 mM; DTT 10 mM; NaN3 0.02%
sample_2: VpR55, [U-5% 13C; U-100% 15N], 1.1 mM; MES 20 mM; NaCl 100 mM; CaCl2 5 mM; DTT 10 mM; NaN3 0.02%
sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 393 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 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY_aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC_high resolution | sample_2 | isotropic | sample_conditions_1 |
Software:
TOPSPIN v1.3, Bruker Biospin - collection
AutoAssign v2.2.1, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment
SPARKY v3.110, Goddard - data analysis, peak picking
AutoStruct v2.1.1, Huang, Tejero, Powers and Montelione - structure solution
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
X-PLOR NIH v2.11.2, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution
PSVS v1.3, Bhattacharya and Montelione - data analysis
PDBStat v4.0, Tejero and Montelione - PDB analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Related Database Links:
| SWS | Q87PC4_VIBPA |
| PDB | |
| DBJ | BAC59856 GAD73629 GAJ70766 GAJ75149 GAK18004 |
| GB | ABU71295 ACY51602 AEX22003 AGQ92134 AGR00117 |
| REF | NP_797972 WP_005377453 WP_005494976 WP_005532367 WP_014231881 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts