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- PDB-1orl: 1H NMR structure determination of Viscotoxin C1 -

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Basic information

Entry
Database: PDB / ID: 1orl
Title1H NMR structure determination of Viscotoxin C1
ComponentsViscotoxin C1
KeywordsTOXIN / helix-turn-helix / beta-sheet / concentric motif of disulphide bridges
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
Viscotoxin-B / Viscotoxin-C1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodSOLUTION NMR / DYANA was employed for structure determination Discover was employed for energy minimisation of DYANA structures
AuthorsMolinari, H. / Romagnoli, S. / Fogolari, F. / Catalano, M. / Urech, K. / Giannattasio, M. / Ragona, L.
Citation
Journal: Biochemistry / Year: 2003
Title: NMR solution structure of viscotoxin C1 from Viscum album species Coloratum ohwi: toward a structure-function analysis of viscotoxins.
Authors: Romagnoli, S. / Fogolari, F. / Catalano, M. / Zetta, L. / Schaller, G. / Urech, K. / Giannattasio, M. / Ragona, L. / Molinari, H.
#1: Journal: Biochem.J. / Year: 2000
Title: NMR structural determination of viscotoxin A3 from Viscum album L.
Authors: Molinari, H. / Romagnoli, S. / Fogolari, F. / Catalano, M. / Urech, K. / Giannattasio, M. / Ragona, L.
History
DepositionMar 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999sequence The author indicated that the primary sequence for this protein has not yet been deposited ...sequence The author indicated that the primary sequence for this protein has not yet been deposited in any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viscotoxin C1


Theoretical massNumber of molelcules
Total (without water)4,9551
Polymers4,9551
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 / 600structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Viscotoxin C1


Mass: 4954.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: viscotoxin C1 has been isolated from european mistletoe leaves
Source: (natural) Viscum album (European mistletoe) / References: UniProt: P08943, UniProt: P83554*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 TOCSY
1212D NOESY
131DQF-COSY
2412D TOCSY
2512D NOESY
261DQF-COSY
1722D TOCSY
1822D NOESY
NMR detailsText: This structure was determined using standard 1H 2D NMR techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM viscotoxin B; phosphate buffer pH 3.6 50mM; 90%H20, 10% D2O90%H20, 10% D2O
20.7 mM viscotoxin B; phosphate buffer pH 3.6 50mM; D2OD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM phosphate buffer 3.6ambient 285 K
250mM phosphate buffer 3.6ambient 295 K
350mM deuterated phosphate buffer 3.6ambient 285 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.4Guentertstructure solution
Discover1997 versionMolecular Simulations, san Diego, CA, USAstructure solution
XwinNMR2.6Brukerprocessing
XEASY1.3Xia and Bartelsdata analysis
Discover1997 versionMolecular Simulations, san Diego, CA, USArefinement
RefinementMethod: DYANA was employed for structure determination Discover was employed for energy minimisation of DYANA structures
Software ordinal: 1
Details: the structures are based on a total of 691 restraints. 631 are NOE-derived distance restraints,(224intraresidues,159 short range, 125 medium range and 123 long range), 18 dihedral angle ...Details: the structures are based on a total of 691 restraints. 631 are NOE-derived distance restraints,(224intraresidues,159 short range, 125 medium range and 123 long range), 18 dihedral angle restraints, 24 for backbone H-bonds and 18 for disulphide bridges. Bond lengths CD-OE2 in glutamic acid residues and CG-OD2 in aspartic acid residues are larger than typical values (as seen in remark 500) because protonated forms were considered due to the low experimental pH.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 10

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