BMRB Entry 16258
Click here to enlarge.
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/BMR16258
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: Solution Structure of RCL PubMed: 19720067
Deposition date: 2009-04-15 Original release date: 2009-09-04
Authors: Doddapaneni, K.; Mahler, B; Yuan, C.; Wu, Z.
Citation: Doddapaneni, Kiran; Mahler, Bryon; Pavlovicz, Ryan; Haushalter, Adam; Yuan, Chunhua; Wu, Zhengrong. "Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase." J. Mol. Biol. 394, 423-434 (2009).
Assembly members:
RCL, polymer, 165 residues, 17799.068 Da.
Natural source: Common Name: Rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
RCL: GHMAASGEQAPCSVYFCGSI
RGGREDQALYARIVSRLRRY
GKVLTEHVADAELEPLGEEA
AGGDQFIHEQDLNWLQQADV
VVAEVTQPSLGVGYELGRAV
ALGKPILCLFRPQSGRVLSA
MIRGAADGSRFQVWDYAEGE
VETMLDRYFEAYLPQKTASS
SHPSA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 634 |
| 15N chemical shifts | 146 |
| 1H chemical shifts | 899 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | RCL_1 | 1 |
| 2 | RCL_2 | 1 |
Entities:
Entity 1, RCL_1 165 residues - 17799.068 Da.
| 1 | GLY | HIS | MET | ALA | ALA | SER | GLY | GLU | GLN | ALA | ||||
| 2 | PRO | CYS | SER | VAL | TYR | PHE | CYS | GLY | SER | ILE | ||||
| 3 | ARG | GLY | GLY | ARG | GLU | ASP | GLN | ALA | LEU | TYR | ||||
| 4 | ALA | ARG | ILE | VAL | SER | ARG | LEU | ARG | ARG | TYR | ||||
| 5 | GLY | LYS | VAL | LEU | THR | GLU | HIS | VAL | ALA | ASP | ||||
| 6 | ALA | GLU | LEU | GLU | PRO | LEU | GLY | GLU | GLU | ALA | ||||
| 7 | ALA | GLY | GLY | ASP | GLN | PHE | ILE | HIS | GLU | GLN | ||||
| 8 | ASP | LEU | ASN | TRP | LEU | GLN | GLN | ALA | ASP | VAL | ||||
| 9 | VAL | VAL | ALA | GLU | VAL | THR | GLN | PRO | SER | LEU | ||||
| 10 | GLY | VAL | GLY | TYR | GLU | LEU | GLY | ARG | ALA | VAL | ||||
| 11 | ALA | LEU | GLY | LYS | PRO | ILE | LEU | CYS | LEU | PHE | ||||
| 12 | ARG | PRO | GLN | SER | GLY | ARG | VAL | LEU | SER | ALA | ||||
| 13 | MET | ILE | ARG | GLY | ALA | ALA | ASP | GLY | SER | ARG | ||||
| 14 | PHE | GLN | VAL | TRP | ASP | TYR | ALA | GLU | GLY | GLU | ||||
| 15 | VAL | GLU | THR | MET | LEU | ASP | ARG | TYR | PHE | GLU | ||||
| 16 | ALA | TYR | LEU | PRO | GLN | LYS | THR | ALA | SER | SER | ||||
| 17 | SER | HIS | PRO | SER | ALA |
Samples:
Aniso_water: sodium phosphate 25 mM; sodium chloride 25 mM; DTT 2 mM; sodium azide 0.02%; Pf1 phage 12%
Iso_water: sodium phosphate 25 mM; sodium chloride 25 mM; DTT 2 mM; sodium azide 0.02%
D20: sodium phosphate 25 mM; sodium chloride 25 mM; DTT 2 mM; sodium azide 0.02%
sample_conditions_1: pH: 6.5; pressure: 1.0 atm; temperature: 303 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N TROSY | Iso_water | isotropic | sample_conditions_1 |
| 3D HNCA | Iso_water | isotropic | sample_conditions_1 |
| 3D HNCACB | Iso_water | isotropic | sample_conditions_1 |
| 3D HNCOCA | Iso_water | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | Iso_water | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | Iso_water | isotropic | sample_conditions_1 |
| 2D 1H-13C ct-HSQC | Iso_water | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY-TROSY | Iso_water | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY-HSQC | D20 | isotropic | sample_conditions_1 |
| 3D 1H-13C-13C HMQC-NOESY-HSQC | D20 | isotropic | sample_conditions_1 |
| 3D 13C-edited NOESY | Iso_water | isotropic | sample_conditions_1 |
| 3D 15N/13C-filtered 13C-edited NOESY | Iso_water | isotropic | sample_conditions_1 |
| 2D 1H-15N TROSY | Aniso_water | anisotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
ProcheckNMR, Laskowski and MacArthur - data analysis
xwinnmr, Bruker Biospin - collection
TOPSPIN, Bruker Biospin - collection
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking, processing
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts