BMRB Entry 30605

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30605
MolProbity Validation Chart

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Title:
SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH1/AA] AND PLASMINOGEN KRINGLE 2
Deposition date:
2019-04-26
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, 87 residues, 10166.340 Da.
entity_2, polymer, 52 residues, 6020.606 Da.

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: Komagataella pastoris   Vector: PPIC9K

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: YVEFSEECMHGSGENYDGKI SKTMSGLECQAWDSQSPHAH GYIPSKFPNKNLKKNYCRNP DRDLRPWCFTTDPNKRWEYC DIPRCAA
entity_2: GSVEKLTADAELQRLKNEAA EEAELERLKSERHDHDKKEA ERKALEDKLADY

Data sets:
Data typeCount
13C chemical shifts569
15N chemical shifts146
1H chemical shifts855

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 87 residues - 10166.340 Da.

1   TYRVALGLUPHESERGLUGLUCYSMETHIS
2   GLYSERGLYGLUASNTYRASPGLYLYSILE
3   SERLYSTHRMETSERGLYLEUGLUCYSGLN
4   ALATRPASPSERGLNSERPROHISALAHIS
5   GLYTYRILEPROSERLYSPHEPROASNLYS
6   ASNLEULYSLYSASNTYRCYSARGASNPRO
7   ASPARGASPLEUARGPROTRPCYSPHETHR
8   THRASPPROASNLYSARGTRPGLUTYRCYS
9   ASPILEPROARGCYSALAALA

Entity 2, entity_2 52 residues - 6020.606 Da.

1   GLYSERVALGLULYSLEUTHRALAASPALA
2   GLULEUGLNARGLEULYSASNGLUALAALA
3   GLUGLUALAGLULEUGLUARGLEULYSSER
4   GLUARGHISASPHISASPLYSLYSGLUALA
5   GLUARGLYSALALEUGLUASPLYSLEUALA
6   ASPTYR

Samples:

sample_1: plasminogen kringle 2, [U-99% 13C; U-99% 15N], 1.0 mM; VEK50[RH1/AA] 1.0 mM; Bis-Tris-d19, [U-2H], 20 mM; DSS 2 ug/mL; sodium azide 2 ug/mL

sample_2: plasminogen kringle 2 1 mM; VEK50[RH1/AA], [U-99% 13C; U-99% 15N], 1 mM; Bis-Tris-d19, [U-2H], 20 mM; DSS 2 ug/mL; sodium azide 2 ug/mL

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

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

Sparky, Goddard - chemical shift assignment

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

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

HADDOCK, Bonvin - 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