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- PDB-1sm7: Solution structure of the recombinant pronapin precursor, BnIb. -

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Basic information

Entry
Database: PDB / ID: 1sm7
TitleSolution structure of the recombinant pronapin precursor, BnIb.
Componentsrecombinant Ib pronapin
KeywordsPLANT PROTEIN / ALL ALPHA-HELIX / RIGHT-HANDED SUPERHELIX
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
Recombinant Ib pronapin
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsPantoja-Uceda, D. / Palomares, O. / Bruix, M. / Villalba, M. / Rodriguez, R. / Rico, M. / Santoro, J.
CitationJournal: Biochemistry / Year: 2004
Title: Solution structure and stability against digestion of rproBnIb, a recombinant 2S albumin from rapeseed: relationship to its allergenic properties.
Authors: Pantoja-Uceda, D. / Palomares, O. / Bruix, M. / Villalba, M. / Rodriguez, R. / Rico, M. / Santoro, J.
History
DepositionMar 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2013Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: recombinant Ib pronapin


Theoretical massNumber of molelcules
Total (without water)12,5441
Polymers12,5441
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)19 / 50structures with the least restraint violations
Representative

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Components

#1: Protein recombinant Ib pronapin


Mass: 12544.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 his4 / References: UniProt: Q8GT96

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1312D COSY
2412D NOESY
2512D TOCSY
2612D COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM rproBnIb; 10mM phosphate buffer; 95% H2O, 5% D2O95% H2O/5% D2O
21.2mM rproBnIb; 10mM phosphate buffer; 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.0 ambient 308 K
23.0 ambient 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DIANA1.5PETER GUNTERTstructure solution
XWINNMRBRUKERprocessing
NMRView5.0.4BRUCE JOHNSONdata analysis
DIANA1.5PETER GUNTERTrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 19

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