BMRB Entry 34826
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34826
MolProbity Validation Chart
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NMR-STAR v3 text file.
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Title: Structure of the dimeric, periplasmic domain of ExbD PubMed: 37609138
Deposition date: 2023-06-14 Original release date: 2023-10-31
Authors: Zinke, M.; Bardiaux, B.; Izadi-Pruneyre, N.
Citation: Zinke, M.; Lejeune, M.; Mechaly, A.; Bardiaux, B.; Boneca, I.; Delepelaire, P.; Izadi-Pruneyre, N.. "Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake." Biorxiv ., .-. (2023).
Assembly members:
entity_1, polymer, 99 residues, 10870.383 Da.
Natural source: Common Name: Serratia marcescens Taxonomy ID: 615 Superkingdom: Bacteria Kingdom: not available Genus/species: Serratia marcescens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pet30(a)+
Entity Sequences (FASTA):
entity_1: SVDIRVDLPASSAKPQPRPE
KPVFLSVKADKQLYVGDQPV
NADQLTSVLDQRTQANKETT
IFFQADKSVDYETLMSVMDT
LRKAGYLKVGLVGMEGAAK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 876 |
| 15N chemical shifts | 198 |
| 1H chemical shifts | 1394 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 1 |
Entities:
Entity 1, unit_1 99 residues - 10870.383 Da.
| 1 | SER | VAL | ASP | ILE | ARG | VAL | ASP | LEU | PRO | ALA | ||||
| 2 | SER | SER | ALA | LYS | PRO | GLN | PRO | ARG | PRO | GLU | ||||
| 3 | LYS | PRO | VAL | PHE | LEU | SER | VAL | LYS | ALA | ASP | ||||
| 4 | LYS | GLN | LEU | TYR | VAL | GLY | ASP | GLN | PRO | VAL | ||||
| 5 | ASN | ALA | ASP | GLN | LEU | THR | SER | VAL | LEU | ASP | ||||
| 6 | GLN | ARG | THR | GLN | ALA | ASN | LYS | GLU | THR | THR | ||||
| 7 | ILE | PHE | PHE | GLN | ALA | ASP | LYS | SER | VAL | ASP | ||||
| 8 | TYR | GLU | THR | LEU | MET | SER | VAL | MET | ASP | THR | ||||
| 9 | LEU | ARG | LYS | ALA | GLY | TYR | LEU | LYS | VAL | GLY | ||||
| 10 | LEU | VAL | GLY | MET | GLU | GLY | ALA | ALA | LYS |
Samples:
sample_1: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N], 1.5 mM
sample_2: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N], 1.5 mM
sample_3: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N; U-95% 2H], 2 mM
sample_4: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N; U-95% 2H; natural abundance], 2 mM
sample_conditions_1: ionic strength: 0.3 mM; pH: 7; pressure: 1 atm; temperature: 293.15 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D hbCBcgcdHD | sample_1 | isotropic | sample_conditions_1 |
| 2D hbCBcgcdceHE | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N TROSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO hydrogen bond detection | sample_3 | isotropic | sample_conditions_1 |
| 3D DOUBLY-FILTERED 1H-13C NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D DOUBLY-FILTERED 1H-15N NOESY | sample_4 | isotropic | sample_conditions_1 |
Software:
CcpNmr Analysis Assign v3.1, Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW - chemical shift assignment
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation
ARIA v2.3.3, Linge, O'Donoghue and Nilges - structure calculation
CcpNmr Analysis v2.5, Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue ED - peak picking
NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis
TALOS-N v4.12, Shen and Bax - data analysis
NMR spectrometers:
- Bruker AVANCE NEO 800 MHz
- Bruker AVANCE III HD 600 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts