BMRB Entry 18283
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR18283
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: Assignment of E coli periplasmic protein YmgD
Deposition date: 2012-02-20 Original release date: 2013-04-15
Authors: Wu, Kuen-Phon; Inouye, Masayori; Baum, Jean
Citation: Wu, Kuen-Phon; Masuda, Hisako; Hsu, Shang-Te; Baum, Jean; Inouye, Masayori. "Solution structure of homodimeric periplasmic protein YmgD in E. coli" J. Biol. Chem. ., .-..
Assembly members:
YmgD, polymer, 90 residues, Formula weight is not available
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):
YmgD: QDYNIKNGLPSETYITCAEA
NEMAKTDSAQVAEIVAVMGN
ASVASRDLKIEQSPELSAKV
VEKLNQVCAKDPQMLLITAI
DDTMRAIGKK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 342 |
| 15N chemical shifts | 96 |
| 1H chemical shifts | 596 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | YmgD, chain 1 | 1 |
| 2 | YmgD, chain 2 | 1 |
Entities:
Entity 1, YmgD, chain 1 90 residues - Formula weight is not available
| 1 | GLN | ASP | TYR | ASN | ILE | LYS | ASN | GLY | LEU | PRO | |
| 2 | SER | GLU | THR | TYR | ILE | THR | CYS | ALA | GLU | ALA | |
| 3 | ASN | GLU | MET | ALA | LYS | THR | ASP | SER | ALA | GLN | |
| 4 | VAL | ALA | GLU | ILE | VAL | ALA | VAL | MET | GLY | ASN | |
| 5 | ALA | SER | VAL | ALA | SER | ARG | ASP | LEU | LYS | ILE | |
| 6 | GLU | GLN | SER | PRO | GLU | LEU | SER | ALA | LYS | VAL | |
| 7 | VAL | GLU | LYS | LEU | ASN | GLN | VAL | CYS | ALA | LYS | |
| 8 | ASP | PRO | GLN | MET | LEU | LEU | ILE | THR | ALA | ILE | |
| 9 | ASP | ASP | THR | MET | ARG | ALA | ILE | GLY | LYS | LYS |
Samples:
CN-YmgD: YmgD, [U-99% 13C; U-99% 15N], 0.4 mM; H2O 90%; D2O 10%; Sodium acetate 100 mM; NaCl 50 mM
pH_5.0: ionic strength: 0.05 M; pH: 5; pressure: 1 atm; temperature: 308 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | CN-YmgD | isotropic | pH_5.0 |
| 2D 1H-13C HSQC | CN-YmgD | isotropic | pH_5.0 |
| 2D 1H-13C HSQC aliphatic | CN-YmgD | isotropic | pH_5.0 |
| 3D HNCO | CN-YmgD | isotropic | pH_5.0 |
| 3D HN(CA)CO | CN-YmgD | isotropic | pH_5.0 |
| 3D C(CO)NH | CN-YmgD | isotropic | pH_5.0 |
| 3D HNCACB | CN-YmgD | isotropic | pH_5.0 |
| 3D H(CCO)NH | CN-YmgD | isotropic | pH_5.0 |
| 3D HCCH-TOCSY | CN-YmgD | isotropic | pH_5.0 |
| 3D CBCA(CO)NH | CN-YmgD | isotropic | pH_5.0 |
| 3D 1H-15N NOESY | CN-YmgD | isotropic | pH_5.0 |
| 3D 1H-15N TOCSY | CN-YmgD | isotropic | pH_5.0 |
| 3D 1H-13C NOESY | CN-YmgD | isotropic | pH_5.0 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment
NMR spectrometers:
- Varian INOVA 800 MHz
Related Database Links:
| PDB | |
| DBJ | BAA36005 BAG76740 BAI24982 BAI30108 BAI35428 |
| EMBL | CAP75703 CAQ31672 CAQ98049 CAR02560 CAR07513 |
| GB | AAC74255 AAN42775 AAN80081 AAP16666 AAZ87885 |
| REF | NP_415689 NP_707068 WP_000219597 WP_000531016 WP_000712685 |
| SP | P0AB46 P0AB47 P0AB48 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts