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- PDB-1l6h: Solution Structure of Plant nsLTP2 purified from Rice (oryza Sativa) -

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Basic information

Entry
Database: PDB / ID: 1l6h
TitleSolution Structure of Plant nsLTP2 purified from Rice (oryza Sativa)
ComponentsNon-Specific Lipid Transfer Protein
KeywordsLIPID TRANSPORT / nsLTP2 / Plant LTP / lipid transfer
Function / homology
Function and homology information


lipid transport / lipid binding
Similarity search - Function
Probable lipid transfer / Non-specific lipid-transfer protein type 2 / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP 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 2 / Non-specific lipid-transfer protein 2
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsSamuel, D. / Lyu, P.-C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Solution structure of plant nonspecific lipid transfer protein-2 from rice (Oryza sativa).
Authors: Samuel, D. / Liu, Y.J. / Cheng, C.S. / Lyu, P.C.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Purification and characterization of a novel 7-kDa non-specific lipid transfer protein-2 from rice (Oryza sativa)
Authors: Liu, Y.-J. / Samuel, D. / Lin, C.-H. / Lyu, P.-C.
History
DepositionMar 11, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4Nov 13, 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: Non-Specific Lipid Transfer Protein


Theoretical massNumber of molelcules
Total (without water)7,0171
Polymers7,0171
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein Non-Specific Lipid Transfer Protein / LTP2


Mass: 7017.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / References: UniProt: P83210, UniProt: Q10ST8*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
131TOCSY

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Sample preparation

DetailsSolvent system: 90% H2O/10% D2O
Sample conditionspH: 6.4 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
XwinNMR2.1Brukercollection
XwinNMR2.1Brukerprocessing
X-PLOR3.8Brugnerstructure solution
X-PLOR3.8Brugnerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was based on a total of 862 distance constraints, 813 are NOE-derived distance constrains, 30 diestance restraints from hydrogen bonds, 19 dihedral angle restrains.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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