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Biological Magnetic Resonance Data Bank


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BMRB Entry 19704

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19704
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Title: Neurotoxin II from snake venom Naja Oxiana in solution

Deposition date: 2013-12-26 Original release date: 2015-01-26

Authors: Lesovoy, Dmitry; Nolde, Svetlana; Bocharov, Eduard; Lyukmanova, Ekaterina; Arseniev, Alexander

Citation: Lesovoy, Dmitry; Nolde, Svetlana; Bocharov, Eduard; Lyukmanova, Ekaterina; Dubinnyi, Maxim; Arseniev, Alexander. "An NMR-based approach for validation of protein side-chains dynamics in silico"  To be Published ., .-..

Assembly members:
entity, polymer, 61 residues, 6895.811 Da.

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

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

Entity Sequences (FASTA):
entity: LECHNQQSSQPPTTKTCSGE TNCYKKWWSDHRGTIIERGC GCPKVKPGVNLNCCRTDRCN N

Data sets:
Data typeCount
13C chemical shifts282
15N chemical shifts83
1H chemical shifts416
H exchange protection factors39
T1 relaxation values666
T2 relaxation values183
coupling constants729
dipole-dipole cross correlation relaxation values381
heteronuclear NOE values657
pKa values8
theoretical chemical shifts1376

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Neurotoxin II1

Entities:

Entity 1, Neurotoxin II 61 residues - 6895.811 Da.

1   LEUGLUCYSHISASNGLNGLNSERSERGLN
2   PROPROTHRTHRLYSTHRCYSSERGLYGLU
3   THRASNCYSTYRLYSLYSTRPTRPSERASP
4   HISARGGLYTHRILEILEGLUARGGLYCYS
5   GLYCYSPROLYSVALLYSPROGLYVALASN
6   LEUASNCYSCYSARGTHRASPARGCYSASN
7   ASN

Samples:

sample_1: Neurotoxin II, [U-99% 13C; U-99% 15N], 1 mM; sodium azide 0.3 mM; citric acid 10 mM; Na2HPO4 20 mM

sample_2: Neurotoxin II, [U-99% 15N], 1 mM; sodium azide 0.3 mM; citric acid 10 mM; Na2HPO4 20 mM

sample_3: Neurotoxin II, [U-99% 15N], 1 mM; sodium azide 0.3 mM; citric acid 10 mM; Na2HPO4 20 mM

sample_4: Neurotoxin II 2 mM; sodium azide 0.3 mM

sample_conditions_1: ionic strength: 50 mM; pH: 5.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C constant time HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C constant time HSQC aromaticsample_1isotropicsample_conditions_1
2D 13C-15N HSQC carbon detectedsample_1isotropicsample_conditions_1
2D 13C->13C carbon detectedsample_1isotropicsample_conditions_1
2D 1H->(13C)->13C carbon detectedsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D HNHBsample_2isotropicsample_conditions_1
2D DQF-COSYsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C(constant time) NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-15N CLEANEXsample_2isotropicsample_conditions_1
3D HNCO modifined for hidrogen bonds detectionsample_1isotropicsample_conditions_1
2D 1H-15N HSQC spectra set for H/D exchangesample_2isotropicsample_conditions_1
2D(1H-15N) spectra set for 15N R1sample_2isotropicsample_conditions_1
2D(1H-15N) spectra set for NH-NH dipolar cross-correlation contribution to 15N R1sample_2isotropicsample_conditions_1
2D(1H-15N) spectra set for 15N R2sample_2isotropicsample_conditions_1
2D(1H-15N) spectra set for 15N-1H NOEsample_2isotropicsample_conditions_1
2D(1H-13C) spectra set for 13C R1sample_1isotropicsample_conditions_1
2D(1H-13C) spectra set for 13C-1H NOEsample_1isotropicsample_conditions_1
2D(1H-13C) spectra set for CH-CH dipolar cross-correlation contribution to 13C R1sample_1isotropicsample_conditions_1
2D(1H-13C) spectra set for CH-CH dipolar cross-correlation contribution to 13C R2sample_1isotropicsample_conditions_1
2D(1H-15N) spectra set for 15N R1sample_3isotropicsample_conditions_1
2D(1H-15N) spectra set for 15N R2sample_3isotropicsample_conditions_1
2D(1H-15N) spectra set for 15N-1H NOEsample_3isotropicsample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CARA v1.8.4, Rochus Keller - chemical shift assignment

Mathematica, Wolfram Research - data analysis

NMRPipe(ACME), Delaglio, Zhengrong and Bax - data analysis, processing

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

PDB
PRF 730936A
UNP P01427
BMRB 16060
SP P01427 P59276

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