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- PDB-2myh: Omega-Tbo-IT1: selective inhibitor of insect calcium channels iso... -

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Basic information

Entry
Database: PDB / ID: 2myh
TitleOmega-Tbo-IT1: selective inhibitor of insect calcium channels isolated from Tibellus oblongus spider venom
ComponentsOmega-Tbo-IT1 toxin
KeywordsTOXIN / cystine knot inhibitor / ICK
Function / homologyhost cell presynaptic membrane / calcium channel regulator activity / toxin activity / extracellular region / Omega-phylotoxin-To1a
Function and homology information
Biological speciesTibellus oblongus (spider)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsAltukhov, D. / Bozin, T. / Bocharov, E. / Kozlov, S. / Mikov, A.
CitationJournal: Sci Rep / Year: 2015
Title: omega-Tbo-IT1-New Inhibitor of Insect Calcium Channels Isolated from Spider Venom.
Authors: Mikov, A.N. / Fedorova, I.M. / Potapieva, N.N. / Maleeva, E.E. / Andreev, Y.A. / Zaitsev, A.V. / Kim, K.K. / Bocharov, E.V. / Bozin, T.N. / Altukhov, D.A. / Lipkin, A.V. / Kozlov, S.A. / ...Authors: Mikov, A.N. / Fedorova, I.M. / Potapieva, N.N. / Maleeva, E.E. / Andreev, Y.A. / Zaitsev, A.V. / Kim, K.K. / Bocharov, E.V. / Bozin, T.N. / Altukhov, D.A. / Lipkin, A.V. / Kozlov, S.A. / Tikhonov, D.B. / Grishin, E.V.
History
DepositionJan 23, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Omega-Tbo-IT1 toxin


Theoretical massNumber of molelcules
Total (without water)4,3481
Polymers4,3481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Omega-Tbo-IT1 toxin


Mass: 4348.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tibellus oblongus (spider) / Plasmid: pET-32-b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0G3F8Z3*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: TWO-DIMENSIONAL 1H-1H DQF-COSY, TOCSY (80-MS MIXING TIME), NOESY (120-MS MIXING TIME) AND 1H-13C HSQC (AT NATURAL ABUNDANCE) NMR SPECTRA OF 1.5 MM RECOMBINANT OMEGA-TBO-IT1 TOXIN ...Details: TWO-DIMENSIONAL 1H-1H DQF-COSY, TOCSY (80-MS MIXING TIME), NOESY (120-MS MIXING TIME) AND 1H-13C HSQC (AT NATURAL ABUNDANCE) NMR SPECTRA OF 1.5 MM RECOMBINANT OMEGA-TBO-IT1 TOXIN (SOLUBILIZED IN H2O OR D2O WITH 20 MM PHOSPHATE BUFFER, PH 5.8) WERE ACQUIRED AT 12C AND 20C ON NMR SPECTROMETER VARIAN NMR SYSTEM 700 MHZ.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC
1422D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM Omega-Tbo-IT1, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM Omega-Tbo-IT1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMOmega-Tbo-IT1-11
1.5 mMOmega-Tbo-IT1-22
Sample conditionsIonic strength: 0.06 / pH: 5.8 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System 700 / Manufacturer: Varian / Model: Uniform NMR System 700 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ACMEDelaglio, Zhengrong and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 422 / NOE intraresidue total count: 249 / NOE long range total count: 49 / NOE medium range total count: 21 / NOE sequential total count: 103 / Disulfide bond constraints total count: 24 / Hydrogen bond constraints total count: 88 / Protein chi angle constraints total count: 89 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 89 / Protein psi angle constraints total count: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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