BMRB Entry 15989
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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/BMR15989
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Title: Solution NMR structure of the R2R3 DNA binding domain of Myb1 protein from protozoan parasite Trichomonas vaginalis PubMed: 19246540
Deposition date: 2008-10-16 Original release date: 2009-04-04
Authors: Lou, Yuan-Chao; Wei, Shu-Yi; Rajasekaran, M.; Chou, Chun-Chi; Hsu, Hong-Ming; Tai, Jung-Hsiang; Chen, Chinpan
Citation: Lou, Yuan-Chao; Wei, Shu-Yi; Rajasekaran, M.; Chou, Chun-Chi; Hsu, Hong-Ming; Tai, Jung-Hsiang; Chen, Chinpan. "NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis" Nucleic Acids Res. 37, 2381-2394 (2009).
Assembly members:
R2R3 DNA binding domain, polymer, 107 residues, 13218.344 Da.
Natural source: Common Name: Trichomonas vaginalis Taxonomy ID: 5722 Superkingdom: Eukaryota Kingdom: not available Genus/species: Trichomonas vaginalis
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
R2R3 DNA binding domain: KVKFTEEEDLKLQQLVMRYG
AKDWIRISQLMITRNPRQCR
ERWNNYINPALRTDPWSPEE
DMLLDQKYAEYGPKWNKISK
FLKNRSDNNIRNRWMMIARH
RAKHQKS
- assigned_chemical_shifts
- heteronucl_NOEs
| Data type | Count |
| 13C chemical shifts | 493 |
| 15N chemical shifts | 121 |
| 1H chemical shifts | 789 |
| heteronuclear NOE values | 92 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | R2R3 DNA binding domain | 1 |
Entities:
Entity 1, R2R3 DNA binding domain 107 residues - 13218.344 Da.
| 1 | LYS | VAL | LYS | PHE | THR | GLU | GLU | GLU | ASP | LEU | ||||
| 2 | LYS | LEU | GLN | GLN | LEU | VAL | MET | ARG | TYR | GLY | ||||
| 3 | ALA | LYS | ASP | TRP | ILE | ARG | ILE | SER | GLN | LEU | ||||
| 4 | MET | ILE | THR | ARG | ASN | PRO | ARG | GLN | CYS | ARG | ||||
| 5 | GLU | ARG | TRP | ASN | ASN | TYR | ILE | ASN | PRO | ALA | ||||
| 6 | LEU | ARG | THR | ASP | PRO | TRP | SER | PRO | GLU | GLU | ||||
| 7 | ASP | MET | LEU | LEU | ASP | GLN | LYS | TYR | ALA | GLU | ||||
| 8 | TYR | GLY | PRO | LYS | TRP | ASN | LYS | ILE | SER | LYS | ||||
| 9 | PHE | LEU | LYS | ASN | ARG | SER | ASP | ASN | ASN | ILE | ||||
| 10 | ARG | ASN | ARG | TRP | MET | MET | ILE | ALA | ARG | HIS | ||||
| 11 | ARG | ALA | LYS | HIS | GLN | LYS | SER |
Samples:
sample_1: entity, [U-13C; U-15N], 1 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 mM; beta-mercaptoethanol 20 mM
sample_2: entity, [U-13C; U-15N], 1 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 mM; beta-mercaptoethanol 20 mM
sample_conditions_1: ionic strength: 0.17 M; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | 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 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HxNOE | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRViewJ v8.0, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking
TALOS, Cornilescu, Delaglio and Bax - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts