BMRB Entry 19768
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19768
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Title: Resonance assignment and secondary structure determination of full length human Dickkopf 4 (hDkk4), a secreted, disulphide-rich Wnt inhibitor protein PubMed: 24816897
Deposition date: 2014-02-05 Original release date: 2015-06-15
Authors: Barkell, Alice; Holdsworth, Gill; Waters, Lorna; Veverka, Vaclav; Slocombe, Patrick; Muskett, Frederick; Henry, Alistair; Robinson, Martyn; Carr, Mark
Citation: Barkell, Alice; Holdsworth, Gill; Waters, Lorna; Muskett, Frederick; Veverka, Vaclav; Slocombe, Patrick; Henry, Alistair; Robinson, Martyn; Carr, Mark. "Resonance assignment and secondary structure determination of full length human Dickkopf 4 (hDkk4), a secreted, disulphide-rich Wnt inhibitor protein" Biomol. NMR Assign. 9, 147-151 (2015).
Assembly members:
hDkk4, polymer, 222 residues, Formula weight is not available
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):
hDkk4: MLVLDFNNIRSSADLHGARK
GSQCLSDTDCNTRKFCLQPR
DEKPFCATCRGLRRRCQRDA
MCCPGTLCVNDVCTTMEDAT
PILERQLDEQDGTHAEGTTG
HPVQENQPKRKPSIKKSQGR
KGQEGESCLRTFDCGPGLCC
ARHFWTKICKPVLLEGQVCS
RRGHKDTAQAPEIFQRCDCG
PGLLCRSQLTSNRQHARLRV
CQKIEKLENLYFQSLEHHHH
HH
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 683 |
15N chemical shifts | 185 |
1H chemical shifts | 1014 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | hDkk4 | 1 |
Entities:
Entity 1, hDkk4 222 residues - Formula weight is not available
1 | MET | LEU | VAL | LEU | ASP | PHE | ASN | ASN | ILE | ARG | ||||
2 | SER | SER | ALA | ASP | LEU | HIS | GLY | ALA | ARG | LYS | ||||
3 | GLY | SER | GLN | CYS | LEU | SER | ASP | THR | ASP | CYS | ||||
4 | ASN | THR | ARG | LYS | PHE | CYS | LEU | GLN | PRO | ARG | ||||
5 | ASP | GLU | LYS | PRO | PHE | CYS | ALA | THR | CYS | ARG | ||||
6 | GLY | LEU | ARG | ARG | ARG | CYS | GLN | ARG | ASP | ALA | ||||
7 | MET | CYS | CYS | PRO | GLY | THR | LEU | CYS | VAL | ASN | ||||
8 | ASP | VAL | CYS | THR | THR | MET | GLU | ASP | ALA | THR | ||||
9 | PRO | ILE | LEU | GLU | ARG | GLN | LEU | ASP | GLU | GLN | ||||
10 | ASP | GLY | THR | HIS | ALA | GLU | GLY | THR | THR | GLY | ||||
11 | HIS | PRO | VAL | GLN | GLU | ASN | GLN | PRO | LYS | ARG | ||||
12 | LYS | PRO | SER | ILE | LYS | LYS | SER | GLN | GLY | ARG | ||||
13 | LYS | GLY | GLN | GLU | GLY | GLU | SER | CYS | LEU | ARG | ||||
14 | THR | PHE | ASP | CYS | GLY | PRO | GLY | LEU | CYS | CYS | ||||
15 | ALA | ARG | HIS | PHE | TRP | THR | LYS | ILE | CYS | LYS | ||||
16 | PRO | VAL | LEU | LEU | GLU | GLY | GLN | VAL | CYS | SER | ||||
17 | ARG | ARG | GLY | HIS | LYS | ASP | THR | ALA | GLN | ALA | ||||
18 | PRO | GLU | ILE | PHE | GLN | ARG | CYS | ASP | CYS | GLY | ||||
19 | PRO | GLY | LEU | LEU | CYS | ARG | SER | GLN | LEU | THR | ||||
20 | SER | ASN | ARG | GLN | HIS | ALA | ARG | LEU | ARG | VAL | ||||
21 | CYS | GLN | LYS | ILE | GLU | LYS | LEU | GLU | ASN | LEU | ||||
22 | TYR | PHE | GLN | SER | LEU | GLU | HIS | HIS | HIS | HIS | ||||
23 | HIS | HIS |
Samples:
sample_1: hDkk4, [U-99% 15N], 200 250 uM; D2O 100%
sample_2: hDkk4, [U-99% 15N], 150 300 uM; H2O 90%; D2O 10%
sample_3: hDkk4, [U-99% 13C; U-99% 15N], 200 300 uM; H2O 90%; D2O 10%
sample_4: hDkk4, [U-99% 13C], 150 250 uM; D2O 100%
sample_conditions_1: pH: 5.5; pressure: 1 atm; temperature: 308 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
2D 1H-15N TROSY | sample_2 | isotropic | sample_conditions_1 |
3D HNCA | sample_3 | isotropic | sample_conditions_1 |
3D HNCACB | sample_3 | isotropic | sample_conditions_1 |
3D HNCO | sample_3 | isotropic | sample_conditions_1 |
3D CBCA(CO)NH | sample_3 | isotropic | sample_conditions_1 |
3D HCCH-TOCSY | sample_4 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY-HSQC | sample_4 | isotropic | sample_conditions_1 |
3D 1H-15N TOCSY-HSQC | sample_2 | isotropic | sample_conditions_1 |
3D 1H-15N NOESY-TROSY | sample_2 | isotropic | sample_conditions_1 |
Software:
TOPSPIN vv3.1, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker DRX 600 MHz
- Bruker Avance 800 MHz
Related Database Links:
DBJ | BAA33438 BAA33475 BAG63095 BAK63662 |
GB | AAF02677 AAI07047 AAI07048 AIC51187 EAW63220 |
REF | NP_055235 XP_001144036 XP_002819091 XP_003269688 XP_003823332 |
SP | Q9UBT3 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts