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- PDB-1tuk: Crystal structure of liganded type 2 non specific lipid transfer ... -

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Basic information

Entry
Database: PDB / ID: 1tuk
TitleCrystal structure of liganded type 2 non specific lipid transfer protein from wheat
ComponentsNonspecific lipid-transfer protein 2G
KeywordsLIPID TRANSPORT / ns-LTP2 / lipid transfer protein
Function / homology
Function and homology information


lipid transport / cell wall organization / lipid binding / extracellular region
Similarity search - Function
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
IODIDE ION / Chem-PGM / Non-specific lipid-transfer protein 2G
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.12 Å
AuthorsHoh, F. / Pons, J.L. / Gautier, M.F. / De Lamotte, F. / Dumas, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a liganded type 2 non-specific lipid-transfer protein from wheat and the molecular basis of lipid binding.
Authors: Hoh, F. / Pons, J.L. / Gautier, M.F. / de Lamotte, F. / Dumas, C.
#1: Journal: J.BIOL.CHEM. / Year: 2003
Title: Refined solution structure of a liganded type 2 wheat nonspecific lipid transfer protein
Authors: Pons, J.L. / de Lamotte, F. / Gautier, M.F. / Delsuc, M.A.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nonspecific lipid-transfer protein 2G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2075
Polymers6,9861
Non-polymers1,2214
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.465, 29.320, 41.550
Angle α, β, γ (deg.)90.00, 127.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nonspecific lipid-transfer protein 2G / ns-LTP2 / LTP2G / Lipid transfer protein 2 isoform 1 / LTP2-1 / 7 kDa lipid transfer protein 1


Mass: 6985.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: P82900
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PGM / 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)] / LYSOPHOSPHATIDYLGLYCEROL


Mass: 483.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H44O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 16, 2002
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.12→32.97 Å / Num. all: 22535 / Num. obs: 22535 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.123→1.153 Å / % possible all: 79.71

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.12→32.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.855 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1097 5.1 %RANDOM
Rwork0.137 ---
all0.138 21350 --
obs0.138 22496 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.37 Å2
2---0.58 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.12→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 44 75 602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021551
X-RAY DIFFRACTIONr_bond_other_d0.0030.02500
X-RAY DIFFRACTIONr_angle_refined_deg1.9372.017738
X-RAY DIFFRACTIONr_angle_other_deg3.49331181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.336566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.85523.63622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.831580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.839154
X-RAY DIFFRACTIONr_chiral_restr0.1280.275
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02590
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02100
X-RAY DIFFRACTIONr_nbd_refined0.3030.2144
X-RAY DIFFRACTIONr_nbd_other0.2470.2491
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2262
X-RAY DIFFRACTIONr_nbtor_other0.0930.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4010.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.660.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3880.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4560.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3131.5339
X-RAY DIFFRACTIONr_mcbond_other1.3251.5138
X-RAY DIFFRACTIONr_mcangle_it3.192533
X-RAY DIFFRACTIONr_scbond_it4.4423225
X-RAY DIFFRACTIONr_scangle_it6.1244.5205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.123→1.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 55 -
Rwork0.253 1269 -
obs--79.71 %

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