BMRB Entry 30153
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30153
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE) PubMed: 27638737
Deposition date: 2016-08-10 Original release date: 2016-11-23
Authors: Evans, R.; Xia, Y.; Wilmot, C.
Citation: Evans, R.; Latham, J.; Klinman, J.; Xia, Y.; Wilmot, C.; Evans, R.; Latham, J.; Klinman, J.; Wilmot, C.; Xia, Y.. "(1)H, (13)C, and (15)N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA" Biomol. NMR Assign. 10, 385-389 (2016).
Assembly members:
entity_1, polymer, 94 residues, 10421.945 Da.
Natural source: Common Name: Methylobacterium extorquens Taxonomy ID: 272630 Superkingdom: Bacteria Kingdom: not available Genus/species: Methylobacterium extorquens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)
Entity Sequences (FASTA):
entity_1: MEPTAFSGSDVPRLPRGVRL
RFDEVRNKHVLLAPERTFDL
DDNAVAVLKLVDGRNTVSQI
AQILGQTYDADPAIIEADIL
PMLAGLAQKRVLER
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 405 |
| 15N chemical shifts | 87 |
| 1H chemical shifts | 647 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 94 residues - 10421.945 Da.
| 1 | MET | GLU | PRO | THR | ALA | PHE | SER | GLY | SER | ASP | ||||
| 2 | VAL | PRO | ARG | LEU | PRO | ARG | GLY | VAL | ARG | LEU | ||||
| 3 | ARG | PHE | ASP | GLU | VAL | ARG | ASN | LYS | HIS | VAL | ||||
| 4 | LEU | LEU | ALA | PRO | GLU | ARG | THR | PHE | ASP | LEU | ||||
| 5 | ASP | ASP | ASN | ALA | VAL | ALA | VAL | LEU | LYS | LEU | ||||
| 6 | VAL | ASP | GLY | ARG | ASN | THR | VAL | SER | GLN | ILE | ||||
| 7 | ALA | GLN | ILE | LEU | GLY | GLN | THR | TYR | ASP | ALA | ||||
| 8 | ASP | PRO | ALA | ILE | ILE | GLU | ALA | ASP | ILE | LEU | ||||
| 9 | PRO | MET | LEU | ALA | GLY | LEU | ALA | GLN | LYS | ARG | ||||
| 10 | VAL | LEU | GLU | ARG |
Samples:
sample_1: PqqD, [U-13C; U-15N], 4.6 mg/mL; potassium phosphate 25 mM
sample_conditions_1: ionic strength: 25 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 2D plane of 3D HCACO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)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 |
| 2D HBCBCGCDHD | sample_1 | isotropic | sample_conditions_1 |
| 2D HBCBCGCDCEHE | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D plane of HCCH-TOCSY for aromatic ring | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N-edited NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C-edited NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe vyear 2012, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
Protein Structure Validation Suite (PSVS) v1.5, http://psvs-1_5-dev.nesg.org/ - refinement
SPARKY v3, Goddard and Kneller - data analysis
TOPSPIN v3.1.6, Bruker Biospin - collection
XPLOR-NIH v2.37, Schwieters - structure calculation
NMR spectrometers:
- Bruker AvanceIII 850 MHz
- Bruker AvanceIII 900 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts