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- PDB-1t12: Solution Structure of a new LTP1 -

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Basic information

Entry
Database: PDB / ID: 1t12
TitleSolution Structure of a new LTP1
ComponentsNONSPECIFIC LIPID-TRANSFER PROTEIN 1
KeywordsLIPID TRANSPORT / cystein rich protein / lipid transfer protein
Function / homology
Function and homology information


response to biotic stimulus / lipid transport / defense response / 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 speciesNicotiana tabacum (common tobacco)
MethodSOLUTION NMR / molecular dynamics
Authorsda Silva, P. / Landon, C. / Industri, B. / Ponchet, M. / Vovelle, F.
CitationJournal: Proteins / Year: 2005
Title: Solution structure of a tobacco lipid transfer protein exhibiting new biophysical and biological features
Authors: da Silva, P. / Landon, C. / Industri, B. / Marais, A. / Marion, D. / Ponchet, M. / Vovelle, F.
History
DepositionApr 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)9,1821
Polymers9,1821
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)10 / 50structures with the lowest restraint energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NONSPECIFIC LIPID-TRANSFER PROTEIN 1 / LTP 1


Mass: 9181.631 Da / Num. of mol.: 1 / Fragment: residues 24-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: LTP1 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q42952

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1413D 15N-separated NOESY
1513D 15N-separated TOCSY
161HNHA
NMR detailsText: The structure was determined using 2D homonuclear and 3D heteronuclear NMR techniques and molecular modelling

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Sample preparation

DetailsContents: 1.8mM tobacco LTP1 15N, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.2 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglioprocessing
NMRViewJohnsondata analysis
ARIABrunger, Lingestructure solution
ARIABrunger, Lingerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: the structure are based on a total of 1526 restraints and 47 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest restraint energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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