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- PDB-1s6d: Structure in solution of a methionine-rich 2S Albumin protein fro... -

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Basic information

Entry
Database: PDB / ID: 1s6d
TitleStructure in solution of a methionine-rich 2S Albumin protein from Sunflower Seed
ComponentsAlbumin 8
KeywordsPLANT PROTEIN / ALL HELIX / FOLDED LEAF / RIGHT-HANDED SUPERHELIX / DISULPHIDE RICH
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / simulated annealing, molecular dynamics in torsion angle space, a final minimization.
AuthorsPantoja-Uceda, D. / Bruix, M. / Shewry, P.R. / Santoro, J. / Rico, M.
CitationJournal: Biochemistry / Year: 2004
Title: Solution Structure of a Methionine-Rich 2S Albumin from Sunflower Seeds: Relationship to Its Allergenic and Emulsifying Properties.
Authors: Pantoja-Uceda, D. / Shewry, P.R. / Bruix, M. / Tatham, A.S. / Santoro, J. / Rico, M.
History
DepositionJan 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin 8


Theoretical massNumber of molelcules
Total (without water)12,1691
Polymers12,1691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50The submitted conformer models are the 20 structures with the lowest target function.
Representative

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Components

#1: Protein Albumin 8 / / Methionine-rich 2S protein / SFA8


Mass: 12169.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Helianthus annuus (common sunflower) / References: UniProt: P23110

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D COSY
1312D TOCSY
1422D NOESY
1522D COSY
1622D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1mM SFA8 unlabeled ;10 mM phosphate buffer ; TSP95% H2O/5% D2O
21.1mM SFA8 unlabeled ;10 mM phosphate buffer ; TSP100% D2O
Sample conditionspH: 3.0 / Temperature: 308 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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBRUKERprocessing
XEASYBartelsdata analysis
DYANA1.5Guntert, P.structure solution
Amber7Caserefinement
RefinementMethod: simulated annealing, molecular dynamics in torsion angle space, a final minimization.
Software ordinal: 1
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest target function.
Conformers calculated total number: 50 / Conformers submitted total number: 20

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