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- PDB-7w9a: Dynamics of lipid displacement inside the hydrophobic cavity of a... -

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Basic information

Entry
Database: PDB / ID: 7w9a
TitleDynamics of lipid displacement inside the hydrophobic cavity of a non-specific lipid transfer protein from Solanum melongena
ComponentsNon-specific lipid-transfer protein
KeywordsLIPID TRANSPORT / nsLTP / Lauric acid / Lipid Transfer Protein / Lipid Binding Dynamics
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 / 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
Similarity search - Domain/homology
LAURIC ACID / Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesSolanum melongena (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMadni, Z.K. / Kumar, A. / Salunke, D.M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2023
Title: Dynamics of lipid displacement inside the hydrophobic cavity of a nonspecific lipid transfer protein from Solanum melongena .
Authors: Madni, Z.K. / Kumar, A. / Kumar, U. / Jaiswal, D. / Salunke, D.M.
History
DepositionDec 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific lipid-transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8053
Polymers9,4051
Non-polymers4012
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.245, 39.245, 94.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Non-specific lipid-transfer protein


Mass: 9404.618 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum melongena (plant) / References: UniProt: A0A247D6Y2
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES at pH 7.5 and 1.5M 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: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 4080 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 38.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.03 / Net I/σ(I): 28.925
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 405 / CC1/2: 0.71 / Rpim(I) all: 0.245 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWM

6iwm


Resolution: 2.12→36.26 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.13
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 209 5.09 %
Rwork0.1962 3899 -
obs0.1986 4080 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.89 Å2
Refinement stepCycle: LAST / Resolution: 2.12→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 28 13 676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028669
X-RAY DIFFRACTIONf_angle_d0.5987902
X-RAY DIFFRACTIONf_chiral_restr0.0432105
X-RAY DIFFRACTIONf_plane_restr0.0057121
X-RAY DIFFRACTIONf_dihedral_angle_d14.8811115
LS refinement shellResolution: 2.12→2.196 Å
RfactorNum. reflection% reflection
Rfree0.2388 209 -
Rwork0.1962 3899 -
obs--99.98 %

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