BMRB Entry 25085
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/BMR25085
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 the rhodanese domain of YgaP from E. coli PubMed: 25204500
Deposition date: 2014-07-12 Original release date: 2014-09-19
Authors: Wang, Wei; Zhou, Peng; Tian, Changlin; Wu, Fangming
Citation: Wang, Wei; Zhou, Peng; He, Yao; Yu, Lu; Xiong, Ying; Tian, Changlin; Wu, Fangming. "Fast conformational exchange between the sulfur-free and persulfide-bound rhodanese domain of E. coli YgaP." Biochem. Biophys. Res. Commun. ., .-. (2014).
Assembly members:
YgaP, polymer, 114 residues, 11660.426 Da.
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
YgaP: MHHHHHHMALTTISPHDAQE
LIARGAKLIDIRDADEYLRE
HIPEADLAPLSVLEQSGLPA
KLRHEQIIFHCQAGKRTSNN
ADKLAAIAAPAEIFLLEDGI
DGWKRAGLPVAVNK
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 724 |
| 13C chemical shifts | 415 |
| 15N chemical shifts | 102 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | rhodanese domain of YgaP | 1 |
Entities:
Entity 1, rhodanese domain of YgaP 114 residues - 11660.426 Da.
| 1 | MET | HIS | HIS | HIS | HIS | HIS | HIS | MET | ALA | LEU | ||||
| 2 | THR | THR | ILE | SER | PRO | HIS | ASP | ALA | GLN | GLU | ||||
| 3 | LEU | ILE | ALA | ARG | GLY | ALA | LYS | LEU | ILE | ASP | ||||
| 4 | ILE | ARG | ASP | ALA | ASP | GLU | TYR | LEU | ARG | GLU | ||||
| 5 | HIS | ILE | PRO | GLU | ALA | ASP | LEU | ALA | PRO | LEU | ||||
| 6 | SER | VAL | LEU | GLU | GLN | SER | GLY | LEU | PRO | ALA | ||||
| 7 | LYS | LEU | ARG | HIS | GLU | GLN | ILE | ILE | PHE | HIS | ||||
| 8 | CYS | GLN | ALA | GLY | LYS | ARG | THR | SER | ASN | ASN | ||||
| 9 | ALA | ASP | LYS | LEU | ALA | ALA | ILE | ALA | ALA | PRO | ||||
| 10 | ALA | GLU | ILE | PHE | LEU | LEU | GLU | ASP | GLY | ILE | ||||
| 11 | ASP | GLY | TRP | LYS | ARG | ALA | GLY | LEU | PRO | VAL | ||||
| 12 | ALA | VAL | ASN | LYS |
Samples:
sample_1: YgaP, [U-100% 13C; U-100% 15N], 0.5 mM; sodium chloride 50 mM; TRIS 20 mM; H2O 90%; D2O 10%
sample_2: YgaP, [U-100% 13C; U-100% 15N], 0.5 mM; sodium chloride 50 mM; TRIS 20 mM; D2O 100%
sample_conditions_1: temperature: 298 K; pH: 7.0; pressure: 1 atm; ionic strength: 0.05 M
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | 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 HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | 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 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, processing
SPARKY, Goddard - peak picking, chemical shift assignment
X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution, refinement
NMR spectrometers:
- Varian INOVA 700 MHz
Related Database Links:
| BMRB | 17137 19943 19946 |
| PDB | |
| DBJ | BAB36952 BAE76780 BAG78445 BAI26930 BAI31960 |
| EMBL | CAQ33005 CAQ87965 CAQ99590 CAR04179 CAR09287 |
| GB | AAC75715 AAG57776 AAN44189 AAN81669 AAP18017 |
| REF | NP_311556 NP_417154 NP_708482 WP_001229433 WP_001229437 |
| SP | P55734 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts