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 50261

Title: Vitronectin hemopexin-like domain with DHPC   PubMed: 32699145

Deposition date: 2020-05-05 Original release date: 2020-07-01

Authors: Shin, Kyungsoo; Kent, James; Singh, Chandan; Fujimoto, Lynn; Yu, Jinghua; Tian, Ye; Im, Wonpil; Marassi, Francesca

Citation: Shin, Kyungsoo; Kent, James; Singh, Chandan; Fujimoto, Lynn; Yu, Jinghua; Tian, Ye; Im, Wonpil; Marassi, Francesca. "Calcium and hydroxyapatite binding site of human vitronectin provides new insights to abnormal deposit formation"  Proc. Natl. Acad. Sci. U.S.A. 117, 18504-18510 (2020).

Assembly members:
entity_1, polymer, 204 residues, Formula weight is not available

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

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

Entity Sequences (FASTA):
entity_1: MELCSGKPFDAFTDLKNGSL FAFRGQYSYELDEKAVRPGY PKLIRDVWGIEGPIDAAFTR INSQGKTYLFKGSQYWRFED GVLDPDYPRNISDGFDGIPD NVDAALALPAHSYSGRERVY FFKGKQYWEYQFQRTSAGTR QPQFISRDWHGVPGQVDAAM AGRISVFFFSGDKYYRVNLR TRRVDTVDPPYPRSIAQYWL GCPA

Data sets:
Data typeCount
13C chemical shifts514
15N chemical shifts174
1H chemical shifts174

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Vitronectin hemopexin-like domain1

Entities:

Entity 1, Vitronectin hemopexin-like domain 204 residues - Formula weight is not available

1   METGLULEUCYSSERGLYLYSPROPHEASP
2   ALAPHETHRASPLEULYSASNGLYSERLEU
3   PHEALAPHEARGGLYGLNTYRSERTYRGLU
4   LEUASPGLULYSALAVALARGPROGLYTYR
5   PROLYSLEUILEARGASPVALTRPGLYILE
6   GLUGLYPROILEASPALAALAPHETHRARG
7   ILEASNSERGLNGLYLYSTHRTYRLEUPHE
8   LYSGLYSERGLNTYRTRPARGPHEGLUASP
9   GLYVALLEUASPPROASPTYRPROARGASN
10   ILESERASPGLYPHEASPGLYILEPROASP
11   ASNVALASPALAALALEUALALEUPROALA
12   HISSERTYRSERGLYARGGLUARGVALTYR
13   PHEPHELYSGLYLYSGLNTYRTRPGLUTYR
14   GLNPHEGLNARGTHRSERALAGLYTHRARG
15   GLNPROGLNPHEILESERARGASPTRPHIS
16   GLYVALPROGLYGLNVALASPALAALAMET
17   ALAGLYARGILESERVALPHEPHEPHESER
18   GLYASPLYSTYRTYRARGVALASNLEUARG
19   THRARGARGVALASPTHRVALASPPROPRO
20   TYRPROARGSERILEALAGLNTYRTRPLEU
21   GLYCYSPROALA

Samples:

sample_1: Vitronectin hemopexin-like domain, [U-100% 13C; U-100% 15N], 90 uM; MES 20 mM; NaCl 300 mM; DHPC 4.5 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 303.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1

Software:

CcpNmr Analysis v2.4.2 - chemical shift assignment, data analysis, peak picking

TALOS-N - data analysis

TOPSPIN - collection, processing

NMR spectrometers:

  • Bruker Avance 600 MHz

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