BMRB Entry 16911

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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/BMR16911
MolProbity Validation Chart

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Title:
Chemical Shift Assignments from PfEMP1: Structured Core
Deposition date:
2010-04-30
Original release date:
2012-01-18
Authors:
Vakonakis, Ioannis; Erat, Michele
Citation:

Citation: Mayer, Christina; Slater, Leanne; Erat, Michele; Konrat, Robert; Vakonakis, Ioannis. "Structural Analysis of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Intracellular Domain Reveals a Conserved Interaction Epitope."  J. Biol. Chem. 287, 7182-7189 (2012).
PubMed: 22249178

Assembly members:

Assembly members:
VARC244, polymer, 81 residues, 9707.9 Da.

Natural source:

Natural source:   Common Name: Plasmodium falciparum   Taxonomy ID: 5833   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: Plasmodium falciparum

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET16b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VARC244: GPLGSMNKFTDDEWNQLKQD FISGILENEQKDLVAKLTNS DPIMNQLDLLHKWLDRHRDM CEKWKSKEDILHKLNEQWNK D

Data sets:
Data typeCount
13C chemical shifts364
15N chemical shifts95
1H chemical shifts604

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1VARC2441

Entities:

Entity 1, VARC244 81 residues - 9707.9 Da.

Sequence corresponds to joining of two distinct regions of the accession

1   GLYPROLEUGLYSERMETASNLYSPHETHR
2   ASPASPGLUTRPASNGLNLEULYSGLNASP
3   PHEILESERGLYILELEUGLUASNGLUGLN
4   LYSASPLEUVALALALYSLEUTHRASNSER
5   ASPPROILEMETASNGLNLEUASPLEULEU
6   HISLYSTRPLEUASPARGHISARGASPMET
7   CYSGLULYSTRPLYSSERLYSGLUASPILE
8   LEUHISLYSLEUASNGLUGLNTRPASNLYS
9   ASP

Samples:

sample_1: VARC244, [U-100% 15N], 1 mM; H2O 95%; D2O, [U-2H], 5%; DTT 1 mM; DSS 0.1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%

sample_2: VARC244, [U-13C; U-15N], 1 mM; H2O 95%; D2O, [U-2H], 5%; DTT 1 mM; DSS 0.1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%

sample_3: VARC244, [U-13C; U-15N], 1 mM; D2O, [U-2H], 100%; DTT 1 mM; DSS 0.1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%

sample_conditions_1: ionic strength: 0.07 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_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 H(CCO)NHsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_3isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
4D 13C-13C NOESYsample_3isotropicsample_conditions_1

Software:

NMRPipe v2.4 Rev 2006.095.11.35, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PIPP v4.3.7, Garrett - chemical shift assignment

Omega Spectrometer Operating Software vBeta 6.03b2, GE/Bruker - collection

NMR spectrometers:

  • Bruker Avance 500 MHz
  • home-built OMEGA 600 MHz
  • home-built OMEGA 500 MHz
  • home-built OMEGA 950 MHz

Related Database Links:

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Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks