BMRB Entry 18541

Name: NMR solution structure of midkine-b, mdkb
Published: 2013-04-02

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PDB ID: 2luu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18541
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of midkine-b, mdkb

Deposition date:

2012-06-21

Original release date:

2013-04-02

Authors:

Yang, Daiwen; Lim, Jackwee; 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-b, polymer, 127 residues, 14021.246 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-b: GSMKKKEKGKEPKADAECSE WQYGKCVPNSGDCGNGIREA TCNEQTKKTKCKVPCNWKKD FGADCKYKFGRWAECDTTTG TRSRSGTLKKALFNAECQTT IKVSKPCTPKTPKPKGGEKK KGKGKEN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	331
15N chemical shifts	115
1H chemical shifts	565

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	midkine-b	1

Entities:

Entity 1, midkine-b 127 residues - 14021.246 Da.

1

GLY

SER

MET

LYS

GLU

LYS

GLY

LYS

2

GLU

PRO

LYS

ALA

ASP

ALA

GLU

CYS

SER

GLU

3

TRP

GLN

TYR

GLY

LYS

CYS

VAL

PRO

ASN

SER

4

GLY

ASP

CYS

GLY

ASN

GLY

ILE

ARG

GLU

ALA

5

THR

CYS

ASN

GLU

GLN

THR

LYS

THR

LYS

6

CYS

LYS

VAL

PRO

CYS

ASN

TRP

LYS

ASP

7

PHE

GLY

ALA

ASP

CYS

LYS

TYR

LYS

PHE

GLY

8

ARG

TRP

ALA

GLU

CYS

ASP

THR

GLY

9

THR

ARG

SER

ARG

SER

GLY

THR

LEU

LYS

10

ALA

LEU

PHE

ASN

ALA

GLU

CYS

GLN

THR

11

ILE

LYS

VAL

SER

LYS

PRO

CYS

THR

PRO

LYS

12

THR

PRO

LYS

PRO

LYS

GLY

GLU

LYS

13

LYS

GLY

LYS

GLY

LYS

GLU

ASN

Samples:

sample_1: potassium phosphate 10 mM; sodium azide 0.1 mM; sodium chloride 100 mM; EDTA 1 mM; midkine-b, [U-100% 13C; U-100% 15N], 0.8 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D MQ-(H)CCH-TOCSY	sample_1	isotropic	sample_conditions_1
4D timeshared 13C/ 15N edited NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement

NMRSpy, Zheng Yu and Yang Daiwen - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

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

NMR spectrometers:

Bruker Avance 500 MHz

PDB	2LUU
GB	AAD38156 AAG27035 AAH59575 ABC67288 AJG05944
REF	NP_571791