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- PDB-5tvi: Crystal structure of non-specific lipid transfer protein reveals ... -

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Basic information

Entry
Database: PDB / ID: 5tvi
TitleCrystal structure of non-specific lipid transfer protein reveals non-canonical lipid binding: possible relevance in modulating allergenicity
Componentsnon specific lipid transfer protein
KeywordsPLANT PROTEIN / Solanum melongena / non-specific lipid transfer protein
Function / homology
Function and homology information


lipid transport / 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
MYRISTIC ACID / octacosan-1-ol / Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesSolanum melongena (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsJain, A. / Salunke, D.M.
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of nonspecific lipid transfer protein from Solanum melongena
Authors: Jain, A. / Salunke, D.M.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: non specific lipid transfer protein
W: non specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5405
Polymers18,8092
Non-polymers7313
Water1,09961
1
V: non specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7253
Polymers9,4051
Non-polymers3202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area4530 Å2
MethodPISA
2
W: non specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8152
Polymers9,4051
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.480, 87.480, 49.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein non specific lipid transfer protein


Mass: 9404.618 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Solanum melongena (plant) / References: UniProt: A0A247D6Y2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-O8N / octacosan-1-ol


Mass: 410.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05M Zinc acetate dihydrate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372, 1.77120
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
21.77121
ReflectionResolution: 1.87→32.826 Å / Num. obs: 18069 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.9
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 5.2 / Num. measured obs: 1171 / CC1/2: 0.939 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Coot0.6model building
PHENIX1.8.1phasing
iMOSFLMdata processing
RefinementMethod to determine structure: SAD / Resolution: 1.87→32.826 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.2254 1804 10.17 %
Rwork0.1836 --
obs0.1877 18041 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→32.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 51 61 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011354
X-RAY DIFFRACTIONf_angle_d1.381815
X-RAY DIFFRACTIONf_dihedral_angle_d19.072520
X-RAY DIFFRACTIONf_chiral_restr0.088211
X-RAY DIFFRACTIONf_plane_restr0.006242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8702-1.89480.30871630.25571222X-RAY DIFFRACTION100
1.8948-1.92070.32221550.23651190X-RAY DIFFRACTION100
1.9207-1.94820.25771660.22561167X-RAY DIFFRACTION100
1.9482-1.97730.24161440.21281208X-RAY DIFFRACTION100
1.9773-2.00810.27911320.21321236X-RAY DIFFRACTION100
2.0081-2.04110.25731190.1931215X-RAY DIFFRACTION100
2.0411-2.07630.24831300.18421235X-RAY DIFFRACTION100
2.0763-2.1140.22681270.19391179X-RAY DIFFRACTION100
2.114-2.15470.19961570.17541237X-RAY DIFFRACTION100
2.1547-2.19860.2651500.1861164X-RAY DIFFRACTION100
2.1986-2.24640.20451270.1671270X-RAY DIFFRACTION100
2.2464-2.29870.24221520.17621181X-RAY DIFFRACTION100
2.2987-2.35610.22061230.17371228X-RAY DIFFRACTION100
2.3561-2.41980.2081260.16351233X-RAY DIFFRACTION100
2.4198-2.4910.19421450.17421215X-RAY DIFFRACTION100
2.491-2.57140.20771460.1671201X-RAY DIFFRACTION100
2.5714-2.66320.20741240.16271214X-RAY DIFFRACTION100
2.6632-2.76980.25531110.17411227X-RAY DIFFRACTION100
2.7698-2.89580.20521450.1831226X-RAY DIFFRACTION100
2.8958-3.04840.1861440.15771187X-RAY DIFFRACTION100
3.0484-3.23920.18881230.17071249X-RAY DIFFRACTION100
3.2392-3.48910.18451270.18321216X-RAY DIFFRACTION100
3.4891-3.83970.24541550.17151196X-RAY DIFFRACTION100
3.8397-4.39420.22941030.18161245X-RAY DIFFRACTION100
4.3942-5.53190.23611360.19891220X-RAY DIFFRACTION100
5.5319-32.83130.24041400.20731159X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 100.6373 Å / Origin y: 32.7485 Å / Origin z: -3.251 Å
111213212223313233
T0.1334 Å20.0434 Å20.0127 Å2-0.1996 Å2-0.0026 Å2--0.1506 Å2
L1.1276 °2-0.3732 °2-0.2292 °2-0.1938 °20.1427 °2--0.0995 °2
S0.1183 Å °-0.0089 Å °0.1276 Å °0.0458 Å °0.0142 Å °-0.0027 Å °0.0279 Å °-0.0528 Å °0.0746 Å °
Refinement TLS groupSelection details: all

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