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- PDB-1nbl: NMR Structure of Hellethionin D -

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Basic information

Entry
Database: PDB / ID: 1nbl
TitleNMR Structure of Hellethionin D
ComponentsHellethionin D
KeywordsTOXIN / Gamma Thionins Helleborus
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 speciesHelleborus purpurascens (plant)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsMilbradt, A.G. / Kerek, F. / Moroder, L. / Renner, C.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Characterization of Hellethionins from Helleborus purpurascens
Authors: Milbradt, A.G. / Kerek, F. / Moroder, L. / Renner, C.
History
DepositionDec 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Remark 999SEQUENCE THERE WAS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hellethionin D


Theoretical massNumber of molelcules
Total (without water)4,9161
Polymers4,9161
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 / 100structures with the lowest energy
Representative

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Components

#1: Protein/peptide Hellethionin D


Mass: 4915.618 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Helleborus purpurascens (plant) / References: UniProt: P60057*PLUS

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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
2412D NOESY
2512D TOCSY
261DQF-COSY
3712D NOESY
3812D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 4mM Hellethionin D; water pH 2.5; 90% H2O, 10% D2O
Solvent system: 90% H2O, 10% D2O pH 2.5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1pH 2.5 2.51 bar293 K
2pH 2.5 2.51 bar283 K
3pH 2.5 2.51 bar303 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 DMXBrukerDMX7501
Bruker DRXBrukerDRX5002
Bruker AMXBrukerAMX4003
Bruker DRXBrukerDRX6004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3brukercollection
XwinNMR3brukerprocessing
Sparky3.98Goddarddata analysis
DGIIAccelrysstructure solution
Discover2.98Accelrysstructure solution
Discover2.98Accelrysrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: Structure is based on 577 NOE-derived constraints and 17 distance constraints from hydrogen bonds
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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