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Basic information

Entry
Database: PDB / ID: 2n8k
TitleChemical Shift Assignments and Structure Determination for spider toxin, U33-theraphotoxin-Cg1c
ComponentsU33-theraphotoxin-Cg1b
KeywordsTOXIN / Disulfide-directed hairpin
Function / homologyLipase, subunit A / Lipase, subunit A / Ribbon / toxin activity / extracellular region / Mainly Beta / U33-theraphotoxin-Cg1b
Function and homology information
Biological speciesChilobrachys guangxiensis (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.-Y. / Pineda, S.S. / Mobli, M. / King, G.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural venomics reveals evolution of a complex venom by duplication and diversification of an ancient peptide-encoding gene.
Authors: Pineda, S.S. / Chin, Y.K. / Undheim, E.A.B. / Senff, S. / Mobli, M. / Dauly, C. / Escoubas, P. / Nicholson, G.M. / Kaas, Q. / Guo, S. / Herzig, V. / Mattick, J.S. / King, G.F.
History
DepositionOct 20, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U33-theraphotoxin-Cg1b


Theoretical massNumber of molelcules
Total (without water)8,1431
Polymers8,1431
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 / 30Stereochemical property by Molprobity
RepresentativeModel #1fewest violations

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Components

#1: Protein U33-theraphotoxin-Cg1b / U33-TRTX-Cg1b / Jingzhaotoxin-71 / JZTX-71


Mass: 8143.156 Da / Num. of mol.: 1 / Fragment: UNP residues 24-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chilobrachys guangxiensis (spider) / Plasmid: pLICC vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B1P1J0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1813D HBHA(CO)NH
1914D HCC(CO)NH-TOCSY

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Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] Cg1c, 10 uM DSS, 5 % sodium azide, 20 mM MES, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMCg1c-1[U-99% 13C; U-99% 15N]1
10 uMDSS-21
5 %sodium azide-31
20 mMMES-41
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance II+ / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
TopSpin3.2Bruker Biospincollection
SparkyGoddardchemical shift assignment
Rowland_NMR_ToolkitHoch JCprocessing nus data
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: Stereochemical property by Molprobity
Conformers calculated total number: 30 / Conformers submitted total number: 20

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