BMRB Entry 30388
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30388
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NMR-STAR v3 text file.
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Title: Solution NMR structure of cysteine-rich calcium bound domains of very low density lipoprotein receptor PubMed: 29965730
Deposition date: 2017-12-21 Original release date: 2018-07-10
Authors: Banerjee, K.; Gruschus, J.; Tjandra, N.; Yakovlev, S.; Medved, L.
Citation: Banerjee, Koyeli; Yakovlev, Sergiy; Gruschus, James; Medved, Leonid; Tjandra, Nico. "Nuclear Magnetic Resonance Solution Structure of the Recombinant Fragment Containing Three Fibrin-Binding Cysteine-Rich Domains of the Very Low Density Lipoprotein Receptor" Biochemistry 57, 4395-4403 (2018).
Assembly members:
entity_1, polymer, 121 residues, 13175.093 Da.
entity_CA, non-polymer, 40.078 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: KTCAESDFVCNNGQCVPSRW
KCDGDPDCEDGSDESPEQCH
MRTCRIHEISCGAHSTQCIP
VSWRCDGENDCDSGEDEENC
GNITCSPDEFTCSSGRCISR
NFVCNGQDDCSDGSDELDCA
P
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 403 |
| 15N chemical shifts | 125 |
| 1H chemical shifts | 647 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2, 1 | 2 |
| 3 | entity_2, 2 | 2 |
| 4 | entity_2, 3 | 2 |
Entities:
Entity 1, entity_1 121 residues - 13175.093 Da.
| 1 | LYS | THR | CYS | ALA | GLU | SER | ASP | PHE | VAL | CYS | ||||
| 2 | ASN | ASN | GLY | GLN | CYS | VAL | PRO | SER | ARG | TRP | ||||
| 3 | LYS | CYS | ASP | GLY | ASP | PRO | ASP | CYS | GLU | ASP | ||||
| 4 | GLY | SER | ASP | GLU | SER | PRO | GLU | GLN | CYS | HIS | ||||
| 5 | MET | ARG | THR | CYS | ARG | ILE | HIS | GLU | ILE | SER | ||||
| 6 | CYS | GLY | ALA | HIS | SER | THR | GLN | CYS | ILE | PRO | ||||
| 7 | VAL | SER | TRP | ARG | CYS | ASP | GLY | GLU | ASN | ASP | ||||
| 8 | CYS | ASP | SER | GLY | GLU | ASP | GLU | GLU | ASN | CYS | ||||
| 9 | GLY | ASN | ILE | THR | CYS | SER | PRO | ASP | GLU | PHE | ||||
| 10 | THR | CYS | SER | SER | GLY | ARG | CYS | ILE | SER | ARG | ||||
| 11 | ASN | PHE | VAL | CYS | ASN | GLY | GLN | ASP | ASP | CYS | ||||
| 12 | SER | ASP | GLY | SER | ASP | GLU | LEU | ASP | CYS | ALA | ||||
| 13 | PRO |
Entity 2, entity_2, 1 - Ca - 40.078 Da.
| 1 | CA |
Samples:
sample_1: VLDLR, [U-99% 15N], 350 uM
sample_2: VLDLR, [U-99% 13C; U-99% 15N], 250 uM
sample_3: VLDLR, [U-99% 13C; U-99% 15N], 250 uM
sample_conditions_1: ionic strength: 100 mM; pH: 6.2; pressure: 760 mmHg; temperature: 306.5 K
sample_conditions_2: ionic strength: 100 mM; pH: 6.2; pressure: 760 mmHg; temperature: 306.5 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_2 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
TOPSPIN, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
Analysis, CCPN - data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts