BMRB Entry 18540

Name: NMR solution structure of midkine-a
Published: 2013-04-02

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PDB ID: 2lut
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18540
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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:

NMR solution structure of midkine-a

Deposition date:

2012-06-21

Original release date:

2013-04-02

Authors:

Lim, Jackwee; Yang, Daiwen; Meng, Dan

Citation:

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).
PubMed: 23418741

Assembly members:

Assembly members:
midkine-a, polymer, 125 residues, 13548.584 Da.

Natural source:

Natural source: Common Name: Zebrafish Taxonomy ID: 7955 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Danio rerio

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-4T-1

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	367
15N chemical shifts	122
1H chemical shifts	628

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	midkine-a	1

Entities:

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

1

GLY

SER

LYS

ASN

LYS

GLU

LYS

ASN

LYS

2

GLY

LYS

GLY

ALA

ASP

CYS

ALA

GLU

3

TRP

LEU

TYR

GLY

SER

CYS

VAL

ALA

ASN

4

GLY

ASP

CYS

GLY

GLN

GLY

MET

ARG

GLU

GLY

5

THR

CYS

ASN

GLU

GLN

THR

ARG

LYS

VAL

LYS

6

CYS

ARG

VAL

PRO

CYS

ASN

TRP

LYS

GLU

7

PHE

GLY

ALA

ASP

CYS

LYS

TYR

LYS

PHE

GLY

8

ASN

TRP

GLY

GLU

CYS

ASP

ALA

THR

SER

9

THR

LYS

SER

ARG

THR

GLY

THR

LEU

GLN

LYS

10

ALA

LEU

PHE

ASN

VAL

GLU

CYS

GLN

THR

11

VAL

SER

VAL

THR

LYS

PRO

CYS

THR

LYS

12

VAL

LYS

ASN

LYS

PRO

LYS

GLY

LYS

GLY

13

LYS

GLY

LYS

GLY

ASN

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample	isotropic	sample_conditions_1
3D HN(CO)CA	sample	isotropic	sample_conditions_1
3D HNCA	sample	isotropic	sample_conditions_1
3D MQ-(H)CCH-TOCSY	sample	isotropic	sample_conditions_1
13C/ 15N edited-NOESY	sample	isotropic	sample_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

PDB	2LUT
GB	AAD38157 AAH71342 AAM27446 AJG05945
REF	NP_571145