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- PDB-1jmp: Solution Structure of the Viscotoxin B -

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Basic information

Entry
Database: PDB / ID: 1jmp
TitleSolution Structure of the Viscotoxin B
Componentsviscotoxin B
KeywordsTOXIN / THIONIN / VISCOTOXIN / VISCUM ALBUM
Function / homology
Function and homology information


defense response / toxin activity / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesViscum album (European mistletoe)
MethodSOLUTION NMR
AuthorsCoulon, A. / Mosbah, A. / Bernard, C. / Rouge, P. / Urech, K. / Darbon, H.
CitationJournal: Biochem.J. / Year: 2003
Title: Comparative membrane interaction study of viscotoxins A3, A2 and B from mistletoe (Viscum album) and connections with their structures
Authors: Coulon, A. / Mosbah, A. / Lopez, A. / Sautereau, A.M. / Schaller, G. / Urech, K. / Rouge, P. / Darbon, H.
History
DepositionJul 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: viscotoxin B


Theoretical massNumber of molelcules
Total (without water)4,8651
Polymers4,8651
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 / 40back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein/peptide viscotoxin B


Mass: 4864.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Viscum album (European mistletoe) / Production host: Escherichia coli (E. coli) / References: UniProt: P08943
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

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Sample preparation

Sample conditionspH: 5 / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Version: 1 / Developer: Brunger / Classification: refinement
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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