BMRB Entry 30603

Name: Solution structure of VEK50 in the bound form with plasminogen kringle 2
Published: 2019-07-18

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PDB ID: 6oq9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30603
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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:

Solution structure of VEK50 in the bound form with plasminogen kringle 2

Deposition date:

2019-04-25

Original release date:

2019-07-18

Authors:

Yuan, Y.; Castellino, F.

Citation:

Citation: Yuan, Yue; Ayinuola, Yetunde; Singh, Damini; Ayinuola, Olawole; Mayfield, Jeffrey; Quek, Adam; Whisstock, James; Law, Ruby; Lee, Shaun; Ploplis, Victoria; Castellino, Francis. "Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes" J. Struct. Biol. 208, 18-29 (2019).
PubMed: 31301349

Assembly members:

Assembly members:
entity_1, polymer, 52 residues, 6173.791 Da.

Natural source:

Natural source: Common Name: Streptococcus pyogenes Taxonomy ID: 1314 Superkingdom: Bacteria Kingdom: not available Genus/species: Streptococcus pyogenes

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSVEKLTADAELQRLKNERH EEAELERLKSERHDHDKKEA ERKALEDKLADY

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	173
15N chemical shifts	50
1H chemical shifts	268

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 52 residues - 6173.791 Da.

1

GLY

SER

VAL

GLU

LYS

LEU

THR

ALA

ASP

ALA

2

GLU

LEU

GLN

ARG

LEU

LYS

ASN

GLU

ARG

HIS

3

GLU

ALA

GLU

LEU

GLU

ARG

LEU

LYS

SER

4

GLU

ARG

HIS

ASP

HIS

ASP

LYS

GLU

ALA

5

GLU

ARG

LYS

ALA

LEU

GLU

ASP

LYS

LEU

ALA

6

ASP

TYR

Samples:

sample_1: VEK50, [U-99% 13C; U-99% 15N], 0.5 ± 0.1 mM; Kringle 2 1.5 ± 0.1 mM; DSS 2 ug/mL; Bis-Tris-d19, [U-2H], 20 mM; sodium azide 2 ug/mL

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

Sparky, Goddard - data analysis

CS-ROSETTA, Shen, Vernon, Baker and Bax - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

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