BMRB Entry 34125

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34125
MolProbity Validation Chart

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Title:
Cytotoxin-1 in DPC-micelle
Deposition date:
2017-04-19
Original release date:
2017-11-30
Authors:
Dubovskii, P.; Dubinnyi, M.; Volynsky, P.; Pustovalova, Y.; Konshina, A.; Utkin, Y.; Efremov, R.; Arseniev, A.
Citation:

Citation: Dubovskii, P.; Dubinnyi, M.; Volynsky, P.; Pustovalova, Y.; Konshina, A.; Utkin, Y.; Arseniev, A.; Efremov, R.; Dubovskii, P.; Lesovoy, D.; Dubinnyi, M.; Konshina, A.; Utkin, Y.; Efremov, R.; Arseniev, A.. "Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin."  J. Biomol. Struct. Dyn. 6, 1-16 (2017).
PubMed: 28990854

Assembly members:

Assembly members:
entity_1, polymer, 60 residues, 6831.339 Da.
entity_HOH, water, 18.015 Da.

Natural source:

Natural source:   Common Name: Central Asian cobra   Taxonomy ID: 8657   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Naja oxiana

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Naja oxiana

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: LKCNKLVPIAYKTCPEGKNL CYKMFMMSDLTIPVKRGCID VCPKNSLLVKYVCCNTDRCN

Data sets:
Data typeCount
1H chemical shifts414

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 60 residues - 6831.339 Da.

1   LEULYSCYSASNLYSLEUVALPROILEALA
2   TYRLYSTHRCYSPROGLUGLYLYSASNLEU
3   CYSTYRLYSMETPHEMETMETSERASPLEU
4   THRILEPROVALLYSARGGLYCYSILEASP
5   VALCYSPROLYSASNSERLEULEUVALLYS
6   TYRVALCYSCYSASNTHRASPARGCYSASN

Entity 2, entity_2 - 18.015 Da.

1   HOH

Samples:

sample_1: D2O, 99.9%-deuterated, 5.5 M; H2O, no, 50 M; HCl, no, 0.01 uM; cytotoxin-1, no, 3.0 mM; dodecylphosphocholine, fully deuterated, 180.0 mM; potassium chloride, no, 50 mM

sample_2: D2O, 100%-deuterated, 55 M; HCl, no, 0.01 uM; cytotoxin-1, no, 3.0 mM; dodecylphosphocholine, fully deuterated, 180.0 mM; potassium chloride, no, 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 bar; temperature: 323 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.0 pD; pressure: 1 bar; temperature: 323 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1not availablesample_conditions_1
2D 1H-1H TOCSYsample_1not availablesample_conditions_1
2D DQF-COSYsample_1not availablesample_conditions_1
diffusionsample_1not availablesample_conditions_1
2D 1H-1H NOESYsample_2not availablesample_conditions_2
2D 1H-1H TOCSYsample_2not availablesample_conditions_2
2D DQF-COSYsample_2not availablesample_conditions_2

Software:

CYANA v1.0.6, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe v2001.085.20.47, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - peak picking

XEASY v1.2.11, Bartels et al. - chemical shift assignment

xwinnmr v2.6, Bruker Biospin - collection

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Varian UNITY 600 MHz