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- PDB-2alg: Crystal structure of peach Pru p3, the prototypic member of the f... -

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Basic information

Entry
Database: PDB / ID: 2alg
TitleCrystal structure of peach Pru p3, the prototypic member of the family of plant non-specific lipid transfer protein pan-allergens
Componentsnon-specific lipid transfer protein
KeywordsLIPID TRANSPORT / Non-specific lipid transfer protein / LTP / ns-LTP / FOOD ALLERGEN
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
LAURIC ACID / HEPTANE / Non-specific lipid-transfer protein 1
Similarity search - Component
Biological speciesPrunus persica (peach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Anomalous Data / Resolution: 2.3 Å
AuthorsPasquato, N. / Berni, R. / Folli, C. / Folloni, S. / Cianci, M. / Pantano, S. / Helliwell, J. / Zanotti, G.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Peach Pru p 3, the Prototypic Member of the Family of Plant Non-specific Lipid Transfer Protein Pan-allergens
Authors: Pasquato, N. / Berni, R. / Folli, C. / Folloni, S. / Cianci, M. / Pantano, S. / Helliwell, J.R. / Zanotti, G.
#1: Journal: Structure / Year: 1995
Title: High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedlings.
Authors: Shin, D.H. / Lee, J.Y. / Hwang, K.Y. / Kim, K.K. / Suh, S.W.
History
DepositionAug 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: non-specific lipid transfer protein
B: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4457
Polymers18,5652
Non-polymers8795
Water2,450136
1
A: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5833
Polymers9,2831
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8614
Polymers9,2831
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: non-specific lipid transfer protein
hetero molecules

B: non-specific lipid transfer protein
hetero molecules

A: non-specific lipid transfer protein
hetero molecules

A: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,88914
Polymers37,1314
Non-polymers1,75810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-5/61
crystal symmetry operation6_554x-y,x,z-1/61
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area8970 Å2
ΔGint-39 kcal/mol
Surface area14770 Å2
MethodPISA
4
B: non-specific lipid transfer protein
hetero molecules

B: non-specific lipid transfer protein
hetero molecules

A: non-specific lipid transfer protein
hetero molecules

A: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,88914
Polymers37,1314
Non-polymers1,75810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_563x,x-y+1,-z-7/61
crystal symmetry operation4_564-x,-y+1,z-1/21
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area7930 Å2
ΔGint-35 kcal/mol
Surface area15810 Å2
MethodPISA
5
B: non-specific lipid transfer protein
hetero molecules

A: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4457
Polymers18,5652
Non-polymers8795
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area3410 Å2
ΔGint-12 kcal/mol
Surface area8460 Å2
MethodPISA
6
B: non-specific lipid transfer protein
hetero molecules

B: non-specific lipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7238
Polymers18,5652
Non-polymers1,1576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-5/61
Buried area1420 Å2
ΔGint-32 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.378, 102.378, 77.295
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-228-

HOH

21B-232-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein non-specific lipid transfer protein


Mass: 9282.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prunus persica (peach) / Gene: LTP / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P81402

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Non-polymers , 5 types, 141 molecules

#2: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-HP6 / HEPTANE / Heptane


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG monomethylether 5000, Mes, Ammonium Sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→51.19 Å / Num. all: 9797 / Num. obs: 9797 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.126 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1448 / Rsym value: 0.446 / % possible all: 91.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: Anomalous Data
Starting model: PDB 1FK5, Modelling model built with Swiss-Model server

1fk5


Resolution: 2.3→51.19 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1365841.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1013 10.4 %RANDOM
Rwork0.204 ---
all0.204 11097 --
obs0.204 9764 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.7077 Å2 / ksol: 0.382099 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å21.13 Å20 Å2
2---1.09 Å20 Å2
3---2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→51.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 51 136 1471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 158 9.7 %
Rwork0.222 1478 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ligand_tot.paramligand_tot.top

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