BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19768

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

Data sets:
Data typeCount
13C chemical shifts683
15N chemical shifts185
1H chemical shifts1014

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1hDkk41

Entities:

Entity 1, hDkk4 222 residues - Formula weight is not available

1   METLEUVALLEUASPPHEASNASNILEARG
2   SERSERALAASPLEUHISGLYALAARGLYS
3   GLYSERGLNCYSLEUSERASPTHRASPCYS
4   ASNTHRARGLYSPHECYSLEUGLNPROARG
5   ASPGLULYSPROPHECYSALATHRCYSARG
6   GLYLEUARGARGARGCYSGLNARGASPALA
7   METCYSCYSPROGLYTHRLEUCYSVALASN
8   ASPVALCYSTHRTHRMETGLUASPALATHR
9   PROILELEUGLUARGGLNLEUASPGLUGLN
10   ASPGLYTHRHISALAGLUGLYTHRTHRGLY
11   HISPROVALGLNGLUASNGLNPROLYSARG
12   LYSPROSERILELYSLYSSERGLNGLYARG
13   LYSGLYGLNGLUGLYGLUSERCYSLEUARG
14   THRPHEASPCYSGLYPROGLYLEUCYSCYS
15   ALAARGHISPHETRPTHRLYSILECYSLYS
16   PROVALLEULEUGLUGLYGLNVALCYSSER
17   ARGARGGLYHISLYSASPTHRALAGLNALA
18   PROGLUILEPHEGLNARGCYSASPCYSGLY
19   PROGLYLEULEUCYSARGSERGLNLEUTHR
20   SERASNARGGLNHISALAARGLEUARGVAL
21   CYSGLNLYSILEGLULYSLEUGLUASNLEU
22   TYRPHEGLNSERLEUGLUHISHISHISHIS
23   HISHIS

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:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
3D 1H-13C NOESY-HSQCsample_4isotropicsample_conditions_1
3D 1H-15N TOCSY-HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESY-TROSYsample_2isotropicsample_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