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- PDB-6iwm: Structural insight into probable lipid transfer mechanism of non-... -

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Basic information

Entry
Database: PDB / ID: 6iwm
TitleStructural insight into probable lipid transfer mechanism of non-specific lipid transfer protein via intermediate structures in Solanum melongena
ComponentsNon-specific lipid-transfer protein
KeywordsLIPID TRANSPORT / nsLTP
Function / homology
Function and homology information


lipid transport / lipid binding
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
Similarity search - Component
Biological speciesSolanum melongena (eggplant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMadni, Z.K. / Salunke, D.M.
CitationJournal: Plant J. / Year: 2020
Title: Structural insights into the lipid transfer mechanism of a non-specific lipid transfer protein.
Authors: Madni, Z.K. / Tripathi, S.K. / Salunke, D.M.
History
DepositionDec 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Non-specific lipid-transfer protein
B: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4008
Polymers18,8092
Non-polymers5916
Water1,51384
1
A: Non-specific lipid-transfer protein
hetero molecules

B: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4008
Polymers18,8092
Non-polymers5916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area1360 Å2
ΔGint-3 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.036, 87.036, 50.342
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 (eggplant) / References: UniProt: A0A247D6Y2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 15253 / % possible obs: 99.9 % / Redundancy: 8.4 % / CC1/2: 0.955 / Rmerge(I) obs: 0.064 / Net I/σ(I): 38.4
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 1507 / CC1/2: 0.748 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TVI

5tvi


Resolution: 1.98→25.13 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.44
RfactorNum. reflection% reflection
Rfree0.2172 754 4.94 %
Rwork0.1856 --
obs0.1874 15253 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 36 84 1409
Refine LS restraintsType: f_angle_d / Dev ideal: 0.93 / Number: 1829
LS refinement shellResolution: 1.98→2.05 Å
RfactorNum. reflection% reflection
Rfree0.2771 158 -
Rwork0.2159 2859 -
obs--99 %

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