BMRB Entry 18541
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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/BMR18541
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Title: NMR solution structure of midkine-b, mdkb PubMed: 23418741
Deposition date: 2012-06-21 Original release date: 2013-04-02
Authors: Yang, Daiwen; Lim, Jackwee; Meng, Dan
Citation: Lim, Jackwee; Yao, Sheng; Graf, Martin; Winkler, Christoph; Yang, Daiwen. "Structure-function analysis of full-length midkine reveals novel residues important for heparin binding and zebrafish embryogenesis." Biochem. J. 451, 407-415 (2013).
Assembly members:
midkine-b, polymer, 127 residues, 14021.246 Da.
Natural source: Common Name: Zebrafish Taxonomy ID: 7955 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Danio rerio
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
midkine-b: GSMKKKEKGKEPKADAECSE
WQYGKCVPNSGDCGNGIREA
TCNEQTKKTKCKVPCNWKKD
FGADCKYKFGRWAECDTTTG
TRSRSGTLKKALFNAECQTT
IKVSKPCTPKTPKPKGGEKK
KGKGKEN
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 331 |
| 15N chemical shifts | 115 |
| 1H chemical shifts | 565 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | midkine-b | 1 |
Entities:
Entity 1, midkine-b 127 residues - 14021.246 Da.
| 1 | GLY | SER | MET | LYS | LYS | LYS | GLU | LYS | GLY | LYS | ||||
| 2 | GLU | PRO | LYS | ALA | ASP | ALA | GLU | CYS | SER | GLU | ||||
| 3 | TRP | GLN | TYR | GLY | LYS | CYS | VAL | PRO | ASN | SER | ||||
| 4 | GLY | ASP | CYS | GLY | ASN | GLY | ILE | ARG | GLU | ALA | ||||
| 5 | THR | CYS | ASN | GLU | GLN | THR | LYS | LYS | THR | LYS | ||||
| 6 | CYS | LYS | VAL | PRO | CYS | ASN | TRP | LYS | LYS | ASP | ||||
| 7 | PHE | GLY | ALA | ASP | CYS | LYS | TYR | LYS | PHE | GLY | ||||
| 8 | ARG | TRP | ALA | GLU | CYS | ASP | THR | THR | THR | GLY | ||||
| 9 | THR | ARG | SER | ARG | SER | GLY | THR | LEU | LYS | LYS | ||||
| 10 | ALA | LEU | PHE | ASN | ALA | GLU | CYS | GLN | THR | THR | ||||
| 11 | ILE | LYS | VAL | SER | LYS | PRO | CYS | THR | PRO | LYS | ||||
| 12 | THR | PRO | LYS | PRO | LYS | GLY | GLY | GLU | LYS | LYS | ||||
| 13 | LYS | GLY | LYS | GLY | LYS | GLU | ASN |
Samples:
sample_1: potassium phosphate 10 mM; sodium azide 0.1 mM; sodium chloride 100 mM; EDTA 1 mM; midkine-b, [U-100% 13C; U-100% 15N], 0.8 mM; H2O 95%; D2O 5%
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D MQ-(H)CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 4D timeshared 13C/ 15N edited NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement
NMRSpy, Zheng Yu and Yang Daiwen - chemical shift assignment
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
NMRPipe v1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMR spectrometers:
- Bruker Avance 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts