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- PDB-3fz3: Crystal Structure of almond Pru1 protein -

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Basic information

Entry
Database: PDB / ID: 3fz3
TitleCrystal Structure of almond Pru1 protein
ComponentsPrunin
KeywordsALLERGEN / tree nut allergen / allergy / Pru1 / prunin / amandin / almond / 11S seed storage protein
Function / homology
Function and homology information


cotyledon development / extraorganismal space / seed development / nutrient reservoir activity / protein hexamerization / metal ion binding
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
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsJin, T.C. / Zhang, Y.Z.
CitationJournal: J.Agric.Food Chem. / Year: 2009
Title: Crystal structure of prunin-1, a major component of the almond (Prunus dulcis) allergen amandin.
Authors: Jin, T. / Albillos, S.M. / Guo, F. / Howard, A. / Fu, T.J. / Kothary, M.H. / Zhang, Y.Z.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prunin
B: Prunin
C: Prunin
D: Prunin
E: Prunin
F: Prunin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,07621
Polymers365,6296
Non-polymers44715
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53820 Å2
ΔGint-300 kcal/mol
Surface area64640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.021, 151.021, 165.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Prunin


Mass: 60938.148 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: seeds / Source: (natural) Prunus dulcis (almond) / References: UniProt: Q43607
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5852.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop8.50.1 M Tris Hydrochloride pH 8.5, 2M Ammonium Sulfate, vapor diffusion, hanging drop, temperature 295K
2982vapor diffusion, hanging drop8.50.1 M Tris Hydrochloride pH 8.5, 2M Ammonium Sulfate, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→36.08 Å / Num. obs: 142516 / % possible obs: 99.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.779
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.4-2.493.80.60897.7
2.49-2.594.50.58698.9
2.59-2.75.10.55899.2
2.7-2.855.60.39199.3
2.85-3.025.80.28899.4
3.02-3.2660.19699.5
3.26-3.586.30.1799.6
3.58-4.16.70.12399.6
4.1-5.177.10.09299.7
5.17-5070.07299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.09 Å
Translation2.5 Å36.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.966 / SU ML: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.229 3818 3 %
Rwork0.172 --
obs0.174 126384 88.7 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 43.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2--1.73 Å20 Å2
3----3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19199 0 15 743 19957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02119570
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.92326509
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61552386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.09424.6781212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.421153175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.03615192
X-RAY DIFFRACTIONr_chiral_restr0.150.22780
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.29048
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.213029
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21069
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2271.511895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.212219064
X-RAY DIFFRACTIONr_scbond_it6.54737830
X-RAY DIFFRACTIONr_scangle_it6.1914.57437
X-RAY DIFFRACTIONr_rigid_bond_restr7.295319725
X-RAY DIFFRACTIONr_sphericity_free8.8153758
X-RAY DIFFRACTIONr_sphericity_bonded4.508319199
LS refinement shellResolution: 2.4→2.47 Å
RfactorNum. reflection% reflection
Rfree0.335 219 -
Rwork0.236 7449 -
obs--75.03 %

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