BMRB Entry 15683
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15683
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 NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli, Northeast Structural Genomics Consortium Target ER553.
Deposition date: 2008-03-14 Original release date: 2008-03-19
Authors: Ramelot, Theresa; Zhao, Li; Hamilton, Kieth; Maglaqui, Melissa; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael
Citation: Ramelot, Theresa; Zhao, Li; Hamilton, Kieth; Maglaqui, Melissa; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael. "Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium Target ER553." . ., .-..
Assembly members:
YiaD, polymer, 149 residues, 16056.109 Da.
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Eubacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
YiaD: YYMDVQEAKLRDKMRGTGVS
VTRSGDNIILNMPNNVTFDS
SSATLKPAGANTLTGVAMVL
KEYPKTAVNVIGYTDSTGGH
DLNMRLSQQRADSVASALIT
QGVDASRIRTQGLGPANPIA
SNSTAEGKAQNRRVEITLSP
LLEHHHHHH
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 596 |
| 15N chemical shifts | 161 |
| 1H chemical shifts | 998 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | YiaD | 1 |
Entities:
Entity 1, YiaD 149 residues - 16056.109 Da.
C-terminal residues 59-199 of YiaD followed by 8 non-native C-terminal residues (LEHHHH)
| 1 | TYR | TYR | MET | ASP | VAL | GLN | GLU | ALA | LYS | LEU | ||||
| 2 | ARG | ASP | LYS | MET | ARG | GLY | THR | GLY | VAL | SER | ||||
| 3 | VAL | THR | ARG | SER | GLY | ASP | ASN | ILE | ILE | LEU | ||||
| 4 | ASN | MET | PRO | ASN | ASN | VAL | THR | PHE | ASP | SER | ||||
| 5 | SER | SER | ALA | THR | LEU | LYS | PRO | ALA | GLY | ALA | ||||
| 6 | ASN | THR | LEU | THR | GLY | VAL | ALA | MET | VAL | LEU | ||||
| 7 | LYS | GLU | TYR | PRO | LYS | THR | ALA | VAL | ASN | VAL | ||||
| 8 | ILE | GLY | TYR | THR | ASP | SER | THR | GLY | GLY | HIS | ||||
| 9 | ASP | LEU | ASN | MET | ARG | LEU | SER | GLN | GLN | ARG | ||||
| 10 | ALA | ASP | SER | VAL | ALA | SER | ALA | LEU | ILE | THR | ||||
| 11 | GLN | GLY | VAL | ASP | ALA | SER | ARG | ILE | ARG | THR | ||||
| 12 | GLN | GLY | LEU | GLY | PRO | ALA | ASN | PRO | ILE | ALA | ||||
| 13 | SER | ASN | SER | THR | ALA | GLU | GLY | LYS | ALA | GLN | ||||
| 14 | ASN | ARG | ARG | VAL | GLU | ILE | THR | LEU | SER | PRO | ||||
| 15 | LEU | LEU | GLU | HIS | HIS | HIS | HIS | HIS | HIS |
Samples:
NC_sample: entity, [U-100% 13C; U-100% 15N], 1.9 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %
NC5_sample: entity, [U-5% 13C; U-100% 15N], 1.3 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %
NC_sample_in_D2O: entity, [U-100% 13C; U-100% 15N], 1.9 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %
sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | NC_sample | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC (arom ct) | NC_sample | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | NC5_sample | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | NC_sample | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | NC_sample | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | NC_sample_in_D2O | isotropic | sample_conditions_1 |
| 3D HNCO | NC_sample | isotropic | sample_conditions_1 |
| 3D HNCA | NC_sample | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | NC_sample | isotropic | sample_conditions_1 |
| 3D HNCACB | NC_sample | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | NC_sample | isotropic | sample_conditions_1 |
| 3D C(CO)NH | NC_sample | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | NC_sample | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | NC_sample | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | NC_sample | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | NC_sample | isotropic | sample_conditions_1 |
| 4D CC NOESY | NC_sample_in_D2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC (arom no ct) | NC_sample | isotropic | sample_conditions_1 |
Software:
NMRPipe vlinux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
VNMR v6.1C, Varian - collection
TOPSPIN v2.1, Bruker Biospin - collection
AutoStruct v2.1.1, Huang, Tejero, Powers and Montelione - data analysis
X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution
CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
SPARKY v3.113, Goddard - data analysis
PSVS v1.3, Bhattacharya and Montelione - structure solution
AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment
NMR spectrometers:
- Varian INOVA 600 MHz
- Bruker AvanceIII 850 MHz
Related Database Links:
| PDB | |
| DBJ | BAB37860 BAE77743 BAG79349 BAI28203 BAI33377 |
| EMBL | CAP78012 CAQ33870 CAR00514 CAR05180 CAR10226 |
| GB | AAB18529 AAG58701 AAN45037 AAN82806 AAP19151 |
| REF | NP_312464 NP_709330 WP_000470321 WP_000495106 WP_000747546 |
| SP | P37665 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts