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- PDB-2lvf: Solution structure of the Brazil Nut 2S albumin Ber e 1 -

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Basic information

Entry
Database: PDB / ID: 2lvf
TitleSolution structure of the Brazil Nut 2S albumin Ber e 1
Components2S albuminPlant lipid transfer proteins
KeywordsALLERGEN / copper binding / hydrophobic interaction
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
Napin/ 2S seed storage protein/Conglutin / 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
2S albumin / 2S sulfur-rich seed storage protein 1
Similarity search - Component
Biological speciesBertholletia excelsa (Brazil nut)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 1
AuthorsRundqvist, L. / Tengel, T. / Zdunek, J. / Schleucher, J. / Alcocer, M.J. / Larsson, G.
CitationJournal: Plos One / Year: 2012
Title: Solution structure, copper binding and backbone dynamics of recombinant Ber e 1-the major allergen from Brazil nut.
Authors: Rundqvist, L. / Tengel, T. / Zdunek, J. / Bjorn, E. / Schleucher, J. / Alcocer, M.J. / Larsson, G.
History
DepositionJul 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2S albumin


Theoretical massNumber of molelcules
Total (without water)13,6491
Polymers13,6491
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)12 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein 2S albumin / Plant lipid transfer proteins


Mass: 13648.980 Da / Num. of mol.: 1 / Fragment: UNP residues 37-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bertholletia excelsa (Brazil nut) / Production host: Pichia pastoris (fungus) / References: UniProt: B6EU55, UniProt: P04403*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N NOESY
1313D 1H-13C NOESY
1413D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] Ber e 1, 20 mM potassium phosphate, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] Ber e 1, 20 mM potassium phosphate, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBer e 1-1[U-15N]1
20 mMpotassium phosphate-21
1 mMsodium azide-31
1 mMBer e 1-4[U-13C; U-15N]2
20 mMpotassium phosphate-52
1 mMsodium azide-62
Sample conditionsIonic strength: 0.02 / pH: 5.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
CcpNmr AnalysisVranken et.alpeak picking
CcpNmr AnalysisVranken et.aldata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Protein ConstructorZdunek, Januszrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1038 / NOE intraresidue total count: 606
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 12 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 6 Å
NMR ensemble rmsDistance rms dev: 0.0683 Å

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