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- PDB-1fk5: STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRA... -

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Basic information

Entry
Database: PDB / ID: 1fk5
TitleSTRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER PROTEIN COMPLEXES WITH OLEIC ACID REVEALED BY HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHY
ComponentsNONSPECIFIC LIPID-TRANSFER PROTEIN
KeywordsLIPID TRANSPORT / protein-lipid complex
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
FORMIC ACID / OLEIC ACID / Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.3 Å
AuthorsHan, G.W. / Lee, J.Y. / Song, H.K. / Shin, D.H. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography.
Authors: Han, G.W. / Lee, J.Y. / Song, H.K. / Chang, C. / Min, K. / Moon, J. / Shin, D.H. / Kopka, M.L. / Sawaya, M.R. / Yuan, H.S. / Kim, T.D. / Choe, J. / Lim, D. / Moon, H.J. / Suh, S.W.
History
DepositionAug 9, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NONSPECIFIC LIPID-TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4835
Polymers9,0621
Non-polymers4214
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.676, 49.717, 69.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NONSPECIFIC LIPID-TRANSFER PROTEIN


Mass: 9062.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P19656
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 3.6-4.8M Na formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 24.5-25.5 ℃
Components of the solutions
*PLUS
Conc.: 3.6-4.8 M / Common name: sodium formate

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.3 Å / Num. obs: 18062 / % possible obs: 75.7 % / Redundancy: 5.17 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. measured all: 93324

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Processing

Software
NameVersionClassification
FUJIBA100 SCANNERdata collection
WEISdata reduction
X-PLORmodel building
SHELXL-97refinement
FUJIBA100 SCANNERdata reduction
WEISdata scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: (PDB CODE:1MZL)

1mzl


Resolution: 1.3→8 Å
RfactorNum. reflection
Rfree0.188 809
Rwork0.135 -
obs0.135 -
all-13391
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 106 179 1525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d2.2
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 2.2

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