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- PDB-1zjq: Solution structure of Jingzhaotoxin-VII -

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Basic information

Entry
Database: PDB / ID: 1zjq
TitleSolution structure of Jingzhaotoxin-VII
ComponentsJingzhaotoxin-VII
KeywordsTOXIN / Inhibitor cystine knot motif
Function / homologyHuwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / toxin activity / extracellular region / U1-theraphotoxin-Cg1a 1
Function and homology information
Biological speciesChilobrachys jingzhao (spider)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
AuthorsLiao, Z.
CitationJournal: TO BE PUBLISHED
Title: Solution structure of Jingzhaotoxin-VII
Authors: Liao, Z.
History
DepositionApr 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Jingzhaotoxin-VII


Theoretical massNumber of molelcules
Total (without water)3,6131
Polymers3,6131
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 / 50structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

#1: Protein/peptide Jingzhaotoxin-VII


Mass: 3613.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chilobrachys jingzhao (spider) / References: UniProt: P0C2X7*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 6mM/L JZTX-VII, 20mM phosphate buffer, DEUTERIUM ACETIC ACID
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 / pH: 4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98processing
X-PLORNIH2.9.6Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on 405 NOE-derived distance constraints, 6 dihedral angle restraints, 9 fake distance restraints from disulfide bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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