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- PDB-2eyc: DMSO refined solution structure of crambin in dpc micelles -

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Basic information

Entry
Database: PDB / ID: 2eyc
TitleDMSO refined solution structure of crambin in dpc micelles
ComponentsCRAMBIN
KeywordsPLANT PROTEIN / CRAMBIN / DPC / MICELLES
Function / homology
Function and homology information


defense response / 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 speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodSOLUTION NMR / simulated annealing
AuthorsAhn, H.C. / Markley, J.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Three-dimensional structure of the water-insoluble protein crambin in dodecylphosphocholine micelles and its minimal solvent-exposed surface.
Authors: Ahn, H.C. / Juranic, N. / Macura, S. / Markley, J.L.
History
DepositionNov 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

Downloads & links

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Assembly

Deposited unit
A: CRAMBIN


Theoretical massNumber of molelcules
Total (without water)4,7381
Polymers4,7381
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 / 20DMSO REFINED STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CRAMBIN


Mass: 4738.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Species: Crambe hispanica / Strain: subsp. abyssinica / Gene: THI2 / Plasmid: PET3A-SN_CRAMBIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P01542
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY

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Sample preparation

DetailsContents: 0.5 MM CRAMBIN U-15N,13C, PH 6.0, 20 MM PHOSPHATE BUFFER, 300MM DPC, 90% H2O, 10% D2O
Solvent system: 20 MM PHOSPHATE BUFFER, 300MM DPC, 90% H2O, 10% D2O
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: AMBIENT / Temperature: 298 K

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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
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.3SCHWIETERSrefinement
XPLOR-NIH2.9.3structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: DMSO REFINED STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 20

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