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 18540

Title: NMR solution structure of midkine-a   PubMed: 23418741

Deposition date: 2012-06-21 Original release date: 2013-04-02

Authors: Lim, Jackwee; Yang, Daiwen; 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-a, polymer, 125 residues, 13548.584 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   Vector: pGEX-4T-1

Entity Sequences (FASTA):
midkine-a: GSKNKKEKNKGGKGGADCAE WLYGSCVANNGDCGQGMREG TCNEQTRKVKCRVPCNWKKE FGADCKYKFGNWGECDAATS TKSRTGTLQKALFNVECQQT VSVTKPCTTKVKNKPKGKKG KGKGN

Data sets:
Data typeCount
13C chemical shifts367
15N chemical shifts122
1H chemical shifts628

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1midkine-a1

Entities:

Entity 1, midkine-a 125 residues - 13548.584 Da.

1   GLYSERLYSASNLYSLYSGLULYSASNLYS
2   GLYGLYLYSGLYGLYALAASPCYSALAGLU
3   TRPLEUTYRGLYSERCYSVALALAASNASN
4   GLYASPCYSGLYGLNGLYMETARGGLUGLY
5   THRCYSASNGLUGLNTHRARGLYSVALLYS
6   CYSARGVALPROCYSASNTRPLYSLYSGLU
7   PHEGLYALAASPCYSLYSTYRLYSPHEGLY
8   ASNTRPGLYGLUCYSASPALAALATHRSER
9   THRLYSSERARGTHRGLYTHRLEUGLNLYS
10   ALALEUPHEASNVALGLUCYSGLNGLNTHR
11   VALSERVALTHRLYSPROCYSTHRTHRLYS
12   VALLYSASNLYSPROLYSGLYLYSLYSGLY
13   LYSGLYLYSGLYASN

Samples:

sample: sodium phosphate 10 mM; sodium azide 0.1 mM; sodium chloride 100 mM; EDTA 1 mM; midkine-a, [U-100% 13C; U-100% 15N], 0.8 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsampleisotropicsample_conditions_1
2D 1H-13C HSQCsampleisotropicsample_conditions_1
3D HN(CO)CAsampleisotropicsample_conditions_1
3D HNCAsampleisotropicsample_conditions_1
3D MQ-(H)CCH-TOCSYsampleisotropicsample_conditions_1
13C/ 15N edited-NOESYsampleisotropicsample_conditions_1

Software:

CYANA v2.1, G ntert P. - refinement

NMRPipe v1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.04, Johnson, One Moon Scientific - data analysis

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

PDB
GB AAD38157 AAH71342 AAM27446 AJG05945
REF NP_571145

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts