BMRB Entry 15158
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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/BMR15158
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Title: Solution structure of the adhesion protein Bd37 from Babesia divergens PubMed: 18035372
Deposition date: 2007-03-02 Original release date: 2008-05-06
Authors: Auguin, Daniel; Yang, Yin-Shan; Lohr, Frank; Arold, Stefan; Schetters, Theo; Precigout, Eric; Gorenflot, Andre; Delbecq, Stephane; Roumestand, Christian
Citation: Delbecq, Stephane; Auguin, Daniel; Yang, Yin-Shan; Lohr, Frank; Arold, Stefan; Schetters, Theo; Precigout, Eric; Gorenflot, Andre; Roumestand, Christian. "The solution structure of the adhesion protein Bd37 from Babesia divergens reveals structural homology with eukaryotic proteins involved in membrane trafficking" J. Mol. Biol. 375, 409-424 (2008).
Assembly members:
Bd37, polymer, 294 residues, 31467.693 Da.
Natural source: Common Name: Babesia Divergens Taxonomy ID: 32595 Superkingdom: Eukaryota Kingdom: not available Genus/species: Babesia Divergens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 847 |
| 15N chemical shifts | 278 |
| 1H chemical shifts | 1543 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Bd37 | 1 |
Entities:
Entity 1, Bd37 294 residues - 31467.693 Da.
| 1 | CYS | THR | ASN | LEU | ASN | GLY | SER | GLN | GLU | PRO | ||||
| 2 | ALA | ALA | ALA | ASN | PRO | VAL | VAL | SER | THR | PRO | ||||
| 3 | GLY | ASN | ASP | ALA | GLN | GLN | ALA | GLY | THR | GLN | ||||
| 4 | GLN | GLY | GLY | ALA | ASN | SER | LYS | SER | VAL | PRO | ||||
| 5 | GLU | GLN | GLN | PRO | GLN | GLN | ALA | ALA | GLY | GLU | ||||
| 6 | THR | THR | ALA | THR | VAL | VAL | VAL | LYS | THR | LEU | ||||
| 7 | ASP | VAL | LEU | ARG | GLY | GLU | LEU | ARG | GLY | GLN | ||||
| 8 | ARG | GLU | ALA | PHE | LEU | SER | GLU | ILE | ILE | LYS | ||||
| 9 | SER | ASP | GLY | PRO | PHE | THR | ILE | LEU | GLN | LEU | ||||
| 10 | VAL | GLY | TYR | LEU | ARG | VAL | VAL | ASP | THR | ASP | ||||
| 11 | LEU | LEU | LEU | LYS | VAL | ASP | SER | THR | LYS | VAL | ||||
| 12 | ASP | GLU | ALA | GLY | LYS | LYS | VAL | LYS | ALA | TYR | ||||
| 13 | LEU | GLU | LYS | ILE | GLY | ILE | ARG | GLY | ASP | SER | ||||
| 14 | VAL | GLU | ALA | ALA | LEU | ASP | ASN | LEU | MET | ILE | ||||
| 15 | LYS | VAL | TYR | GLU | ILE | THR | LYS | GLY | THR | VAL | ||||
| 16 | GLU | SER | SER | ALA | GLN | GLY | THR | ASP | SER | GLU | ||||
| 17 | GLU | LEU | LYS | THR | LEU | LEU | LEU | LYS | PHE | SER | ||||
| 18 | GLU | ASP | LEU | LYS | ALA | GLU | GLN | GLU | LEU | HIS | ||||
| 19 | SER | GLU | ALA | LYS | GLY | GLY | GLU | ALA | LEU | LEU | ||||
| 20 | SER | SER | MET | LYS | THR | GLN | HIS | ASP | GLU | LEU | ||||
| 21 | LEU | LYS | LYS | PHE | ALA | ALA | LEU | THR | PRO | THR | ||||
| 22 | PHE | LEU | THR | SER | GLU | ASP | ILE | SER | GLY | TYR | ||||
| 23 | LEU | THR | VAL | PRO | GLU | TYR | GLY | ALA | PRO | MET | ||||
| 24 | ASN | ALA | ALA | LYS | TRP | LYS | LYS | VAL | GLU | GLY | ||||
| 25 | MET | ILE | HIS | GLY | LYS | LEU | GLU | SER | SER | GLU | ||||
| 26 | VAL | PRO | ALA | ASN | LEU | LYS | ALA | LEU | VAL | ALA | ||||
| 27 | GLU | LEU | ILE | GLU | LEU | ARG | GLU | GLN | MET | MET | ||||
| 28 | ASP | LEU | LEU | TYR | GLY | PRO | ILE | GLY | HIS | HIS | ||||
| 29 | ASP | CYS | ALA | ALA | GLY | SER | GLY | GLN | GLY | SER | ||||
| 30 | SER | LYS | LEU | ASN |
Samples:
sample_1: Bd37, [U-99% 15N], 0.5 – 1 mM; phosphate buffer 20 mM; NaCl 50 mM
sample_2: Bd37, [U-99% 13C; U-99% 15N], 0.5 – 1 mM; phosphate buffer 20 mM; NaCl 50 mM
sample_3: Bd37, [13C]-I,V,L methyl, 0.5 – 1 mM; phosphate buffer 20 mM; NaCl 50 mM
sample_conditions_1: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 310 K
sample_conditions_2: pD: 6.8
sample_conditions_3: pH: 6.8
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | anisotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | anisotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | anisotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | sample_1 | anisotropic | sample_conditions_2 |
| (in-phase/antiphase) [15N-1H] HSQC | sample_1 | isotropic | sample_conditions_3 |
Software:
PREDITOR v1, (PREDITOR) Berjanskii - geometry optimization
CINDY, PADILLA - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER v8, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Koll - refinement
GIFA v4, Delsuc - processing
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
NMR spectrometers:
- Bruker Avance 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts