BMRB Entry 15628
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15628
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Title: Solution structure of S. aureus PrsA-PPIase PubMed: 19309529
Deposition date: 2008-01-21 Original release date: 2009-04-01
Authors: Seppala, Raili; Tossavainen, Helena; Heikkinen, Sami; Koskela, Harri; Kontinen, Vesa; Permi, Perttu
Citation: Heikkinen, Outi; Seppala, Raili; Tossavainen, Helena; Heikkinen, Sami; Koskela, Harri; Permi, Perttu; Kilpelainen, Ilkka. "Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA--implications for the catalytic mechanism of parvulins." BMC Struct. Biol. 9, 17-17 (2009).
Assembly members:
PrsA-PPIase, polymer, 111 residues, 12216.032 Da.
Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
PrsA-PPIase: GPLGSDSKKASHILIKVKSK
KSDKEGLDDKEAKQKAEEIQ
KEVSKDPSKFGEIAKKESMD
TGSAKKDGELGYVLKGQTDK
DFEKALFKLKDGEVSEVVKS
SFGYHIIKADK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 484 |
| 15N chemical shifts | 110 |
| 1H chemical shifts | 785 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | PrsA-PPIase | 1 |
Entities:
Entity 1, PrsA-PPIase 111 residues - 12216.032 Da.
GPLGS - cloning artifact
| 1 | GLY | PRO | LEU | GLY | SER | ASP | SER | LYS | LYS | ALA | ||||
| 2 | SER | HIS | ILE | LEU | ILE | LYS | VAL | LYS | SER | LYS | ||||
| 3 | LYS | SER | ASP | LYS | GLU | GLY | LEU | ASP | ASP | LYS | ||||
| 4 | GLU | ALA | LYS | GLN | LYS | ALA | GLU | GLU | ILE | GLN | ||||
| 5 | LYS | GLU | VAL | SER | LYS | ASP | PRO | SER | LYS | PHE | ||||
| 6 | GLY | GLU | ILE | ALA | LYS | LYS | GLU | SER | MET | ASP | ||||
| 7 | THR | GLY | SER | ALA | LYS | LYS | ASP | GLY | GLU | LEU | ||||
| 8 | GLY | TYR | VAL | LEU | LYS | GLY | GLN | THR | ASP | LYS | ||||
| 9 | ASP | PHE | GLU | LYS | ALA | LEU | PHE | LYS | LEU | LYS | ||||
| 10 | ASP | GLY | GLU | VAL | SER | GLU | VAL | VAL | LYS | SER | ||||
| 11 | SER | PHE | GLY | TYR | HIS | ILE | ILE | LYS | ALA | ASP | ||||
| 12 | LYS |
Samples:
sample_1: PrsA-PPIase, [U-15N], 0.3 mM; Bis-TRIS 20 mM; sodium azide 1 mM; EDTA 1 mM
sample_2: PrsA-PPIase, [U-15N], 1 mM; Bis-TRIS 20 mM; sodium azide 1 mM; EDTA 1 mM
sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 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 CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | 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 iHNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY (AROM) | sample_1 | isotropic | sample_conditions_1 |
| (H )C (C C )H | sample_1 | isotropic | sample_conditions_1 |
| (H )C (C C C )H | sample_1 | isotropic | sample_conditions_1 |
| J(CN) intensity modulated constant time 13C-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D R1 resolved 1H-15N-HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D R2 resolved 1H-15N-HSQC | sample_2 | isotropic | sample_conditions_1 |
| exchange rate resolved 1H-15N-HSQC | sample_2 | isotropic | sample_conditions_1 |
Software:
VNMR v6.1C, Varian - collection, processing
SPARKY v3.110, Goddard - chemical shift assignment, data analysis, peak picking
TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER v8.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
ProcheckNMR, Laskowski and MacArthur - quality control
What_check, Vriend - quality control
NMR spectrometers:
- Varian INOVA 800 MHz
- Varian INOVA 600 MHz
- Varian INOVA 500 MHz
- Bruker DRX 500 MHz
Related Database Links:
| PDB | |
| DBJ | BAB42927 BAB58003 BAB95647 BAF68005 BAF78709 |
| EMBL | CAG40919 CAG43567 CAI81463 CAQ50323 CBI49709 |
| GB | AAW36910 ABD22844 ABD31031 ABQ49679 ABR52762 |
| REF | WP_000295838 WP_000315644 WP_000782118 WP_000782119 WP_000782120 |
| SP | A6QI23 A6U2U4 A7X3U8 A8YY10 P60747 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts