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- PDB-3c3v: Crystal structure of peanut major allergen ara h 3 -

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Basic information

Entry
Database: PDB / ID: 3c3v
TitleCrystal structure of peanut major allergen ara h 3
ComponentsArachin Arah3 isoform
KeywordsALLERGEN / peanut allergen / allergy / ara h 3 / glycinin
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Arachin Arah3 isoform
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.73 Å
AuthorsJin, T. / Zhang, Y.
CitationJournal: Mol.Immunol. / Year: 2009
Title: Crystal structure of Ara h 3, a major allergen in peanut.
Authors: Jin, T. / Guo, F. / Chen, Y.W. / Howard, A. / Zhang, Y.Z.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arachin Arah3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5782
Polymers58,5551
Non-polymers231
Water5,134285
1
A: Arachin Arah3 isoform
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)351,46612
Polymers351,3286
Non-polymers1386
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area53140 Å2
ΔGint-266 kcal/mol
Surface area63230 Å2
MethodPISA
2
A: Arachin Arah3 isoform
hetero molecules

A: Arachin Arah3 isoform
hetero molecules

A: Arachin Arah3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,7336
Polymers175,6643
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area17740 Å2
ΔGint-104 kcal/mol
Surface area40450 Å2
MethodPISA
3
A: Arachin Arah3 isoform
hetero molecules

A: Arachin Arah3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1554
Polymers117,1092
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area5370 Å2
ΔGint-30 kcal/mol
Surface area33420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.929, 144.929, 86.924
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-853-

HOH

21A-857-

HOH

31A-870-

HOH

DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: x,y,z ; -y,x-y,z ; -x,y-x,-z ; -y,-x,1/2-z; and y-x,y,1/2-z;

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Components

#1: Protein Arachin Arah3 isoform


Mass: 58554.723 Da / Num. of mol.: 1 / Fragment: UNp residues 21-530 / Source method: isolated from a natural source / Details: seeds / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: B5TYU1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS THE CORRECT RESIDUE AT THIS POSITION IS HISTIDINE

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium Acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 55487 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.6 / Redundancy: 10.2 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 14.4
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.61 / Num. unique all: 5014 / % possible all: 90.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.73→41.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.409 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2631 5.1 %RANDOM
Rwork0.186 49465 --
obs0.189 52096 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.2 Å2 / Biso mean: 36.219 Å2 / Biso min: 15.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.73→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 1 285 3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223366
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9354596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31524.627201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47415540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7041530
X-RAY DIFFRACTIONr_chiral_restr0.1770.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022737
X-RAY DIFFRACTIONr_nbd_refined0.2260.21466
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2193
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.246
X-RAY DIFFRACTIONr_mcbond_it2.1941.52041
X-RAY DIFFRACTIONr_mcangle_it3.26323306
X-RAY DIFFRACTIONr_scbond_it4.48931354
X-RAY DIFFRACTIONr_scangle_it6.5934.51274
X-RAY DIFFRACTIONr_rigid_bond_restr3.14533395
X-RAY DIFFRACTIONr_sphericity_free11.0213286
X-RAY DIFFRACTIONr_sphericity_bonded10.80533277
LS refinement shellResolution: 1.73→1.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 143 -
Rwork0.302 2741 -
all-2884 -
obs--70.5 %

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