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- PDB-1siy: NMR structure of mung bean non-specific lipid transfer protein 1 -

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Basic information

Entry
Database: PDB / ID: 1siy
TitleNMR structure of mung bean non-specific lipid transfer protein 1
ComponentsNonspecific lipid-transfer protein 1
KeywordsLIPID BINDING PROTEIN / alpha helix
Function / homology
Function and homology information


lipid transport / defense response to fungus / killing of cells of another organism / defense response to Gram-positive bacterium / lipid binding / membrane
Similarity search - Function
Plant lipid transfer proteins signature. / Plant non-specific lipid-transfer protein/Par allergen / 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
Non-specific lipid-transfer protein 1
Similarity search - Component
Biological speciesVigna radiata var. radiata (mung bean)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLin, K.F. / Liu, Y.N. / Hsu, S.T.D. / Samuel, D. / Cheng, C.S. / Bonvin, A.M.J.J. / Lyu, P.C.
CitationJournal: Biochemistry / Year: 2005
Title: Characterization and Structural Analyses of Nonspecific Lipid Transfer Protein 1 from Mung Bean
Authors: Lin, K.F. / Liu, Y.N. / Hsu, S.T.D. / Samuel, D. / Cheng, C.S. / Bonvin, A.M.J.J. / Lyu, P.C.
History
DepositionMar 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: 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
Revision 1.4Oct 23, 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

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Assembly

Deposited unit
A: Nonspecific lipid-transfer protein 1


Theoretical massNumber of molelcules
Total (without water)9,3081
Polymers9,3081
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)15 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Nonspecific lipid-transfer protein 1 / LTP 1 / NS-LTP1


Mass: 9307.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / Species: Vigna radiata / Strain: var. radiata / References: UniProt: P83434
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 3mM LTP1; 20mM phosphate buffer Na / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM / pH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukerprocessing
X-PLOR3.8Brungerstructure solution
ARIA2Nilgesstructure solution
Sparky3Goddard, Knellerdata analysis
ARIA2Nilgesrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: Structures are calculated from 1675 assigned NOE. 4 disulfide bonds are shown
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 15

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