BMRB Entry 19768

Name: Resonance assignment and secondary structure determination of full length human Dickkopf 4 (hDkk4), a secreted, disulphide-rich Wnt inhibitor protein
Published: 2015-06-15

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19768

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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

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:

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).
PubMed: 24816897

Assembly members:

Assembly members:
hDkk4, polymer, 222 residues, Formula weight is not available

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pLEICS05

Entity Sequences (FASTA):

Entity Sequences (FASTA):
hDkk4: MLVLDFNNIRSSADLHGARK GSQCLSDTDCNTRKFCLQPR DEKPFCATCRGLRRRCQRDA MCCPGTLCVNDVCTTMEDAT PILERQLDEQDGTHAEGTTG HPVQENQPKRKPSIKKSQGR KGQEGESCLRTFDCGPGLCC ARHFWTKICKPVLLEGQVCS RRGHKDTAQAPEIFQRCDCG PGLLCRSQLTSNRQHARLRV CQKIEKLENLYFQSLEHHHH HH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	683
15N chemical shifts	185
1H chemical shifts	1014

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

ILE

ARG

2

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

CYS

GLN

ARG

ASP

ALA

7

MET

CYS

PRO

GLY

THR

LEU

CYS

VAL

ASN

8

ASP

VAL

CYS

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

GLY

11

HIS

PRO

VAL

GLN

GLU

ASN

GLN

PRO

LYS

ARG

12

LYS

PRO

SER

ILE

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

15

ALA

ARG

HIS

PHE

TRP

THR

LYS

ILE

CYS

LYS

16

PRO

VAL

LEU

GLU

GLY

GLN

VAL

CYS

SER

17

ARG

GLY

HIS

LYS

ASP

THR

ALA

GLN

ALA

18

PRO

GLU

ILE

PHE

GLN

ARG

CYS

ASP

CYS

GLY

19

PRO

GLY

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

23

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

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks