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- PDB-1ed0: NMR structural determination of viscotoxin A3 from Viscum album L. -

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Basic information

Entry
Database: PDB / ID: 1ed0
TitleNMR structural determination of viscotoxin A3 from Viscum album L.
ComponentsVISCOTOXIN A3
KeywordsTOXIN / THIONIN / CONCENTRIC MOTIF / HELIX-TURN-HELIX / ALPHA-BETA PROTEIN / AMPHIPATHIC HELIX
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 / RESTRAINED SIMULATED ANNEALING IN TORSION ANGLE SPACE, ITERATIVE RESTRAINTS REFINEMENT, RESTRAINED MOLECULAR DYNAMICS IN CARTESIAN COORDINATE SPACE MINIMIZATION
AuthorsRomagnoli, S. / Ugolini, R. / Fogolari, F. / Schaller, G. / Urech, K. / Giannattasio, M. / Ragona, L. / Molinari, H.
CitationJournal: Biochem.J. / Year: 2000
Title: NMR structural determination of viscotoxin A3 from Viscum album L.
Authors: Romagnoli, S. / Ugolini, R. / Fogolari, F. / Schaller, G. / Urech, K. / Giannattasio, M. / Ragona, L. / Molinari, H.
History
DepositionJan 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 1.4Nov 6, 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 A3


Theoretical massNumber of molelcules
Total (without water)4,8431
Polymers4,8431
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)10 / 600target function
RepresentativeModel #8lowest average rmsd with other structures in the ensemble

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Components

#1: Protein/peptide VISCOTOXIN A3


Mass: 4842.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P01538
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
121DQF-COSY
131TOCSY
1422D NOESY
152DQF-COSY
162TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM / pH: 3.6 / Pressure: ambient / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
DYANA1.4Guentert, Wuethrichstructure solution
Discover98MSIrefinement
XwinNMR1.2Bruker Spectrospincollection
XEASY1.2Eccles, Xia, Bartels, Guentert, Billeter, Wuethrichdata analysis
RefinementMethod: RESTRAINED SIMULATED ANNEALING IN TORSION ANGLE SPACE, ITERATIVE RESTRAINTS REFINEMENT, RESTRAINED MOLECULAR DYNAMICS IN CARTESIAN COORDINATE SPACE MINIMIZATION
Software ordinal: 1
Details: 1010 distance restraints were calculated reduced to 734 (230 intraresidue, 172 sequential, 191 medium range, 141 long range) after removal of irrelevant restraints. Calculation started with ...Details: 1010 distance restraints were calculated reduced to 734 (230 intraresidue, 172 sequential, 191 medium range, 141 long range) after removal of irrelevant restraints. Calculation started with 200 randomized conformers and consistently violated restraints were checked and relaxed where necessary. This procedure was repeated until no consistent violations were found in half or more of the structures. 600 new calculations were started and the 20 structures with lowest target function were analyzed. The structure with lowest target function and the structure exhibiting the largest RMSD with it were subjected to restrained molecular dynamics (20 cycles of 15 ps restrained molecular dynamics followed by minimization). All even structures from the last 10 minimized structures were retained from both sets and deposited.
NMR representativeSelection criteria: lowest average rmsd with other structures in the ensemble
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 10

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