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- PDB-8uai: Crystal structure of hetero hexameric hazelnut allergen Cor a 9 -

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Basic information

Entry
Database: PDB / ID: 8uai
TitleCrystal structure of hetero hexameric hazelnut allergen Cor a 9
Components(11S globulin ...) x 3
KeywordsALLERGEN / food allergen / 11S / seed storage protein / iso-allergen / heterohexamers
Function / homology
Function and homology information


seed development / 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 / RmlC-like jelly roll fold
Similarity search - Domain/homology
11S globulin-like protein
Similarity search - Component
Biological speciesCorylus avellana (European hazelnut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhang, Y.Z. / Guo, F.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA) United States
CitationJournal: Plant Physiol Biochem. / Year: 2024
Title: Crystal structure of hetero hexameric 11S seed storage protein of hazelnut.
Authors: Guo, F. / Zhang, Y. / Howard, A. / Xu, Y.
History
DepositionSep 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 11S globulin 1
B: 11S globulin 2
C: 11S globulin 3
D: 11S globulin 1
E: 11S globulin 2
F: 11S globulin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,49424
Polymers338,9496
Non-polymers1,54418
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58850 Å2
ΔGint-144 kcal/mol
Surface area67570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.168, 91.093, 74.854
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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11S globulin ... , 3 types, 6 molecules ADBECF

#1: Protein 11S globulin 1


Mass: 56750.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Corylus avellana (European hazelnut) / References: UniProt: Q8W1C2
#2: Protein 11S globulin 2


Mass: 56479.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Corylus avellana (European hazelnut)
#3: Protein 11S globulin 3


Mass: 56245.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Corylus avellana (European hazelnut)

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Non-polymers , 3 types, 635 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein drops: 5 mM Tris pH 8.0, 0.M M NaCl. Well solution: 0.2M NaCl

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 142012 / % possible obs: 94.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 31.73 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rpim(I) all: 0.063 / Rrim(I) all: 0.111 / Net I/σ(I): 10
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 7049 / CC1/2: 0.725 / CC star: 0.917 / Rpim(I) all: 0.381 / Rrim(I) all: 0.661 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v722data reduction
HKL-2000v722data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→45.8 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 7119 5.01 %
Rwork0.1736 134847 -
obs0.176 141966 92.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.44 Å2
Refinement stepCycle: LAST / Resolution: 1.92→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19136 0 98 617 19851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008320001
X-RAY DIFFRACTIONf_angle_d0.986927098
X-RAY DIFFRACTIONf_chiral_restr0.06512925
X-RAY DIFFRACTIONf_plane_restr0.00953688
X-RAY DIFFRACTIONf_dihedral_angle_d6.86922839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.940.3128980.22161961X-RAY DIFFRACTION40.41
1.94-1.960.29192200.23274370X-RAY DIFFRACTION89.84
1.96-1.990.29452410.22924469X-RAY DIFFRACTION93.56
1.99-2.010.30042390.22394503X-RAY DIFFRACTION93.07
2.01-2.040.24372520.20494519X-RAY DIFFRACTION93.86
2.04-2.070.27612490.20024508X-RAY DIFFRACTION93.02
2.07-2.10.26332860.20424452X-RAY DIFFRACTION93.58
2.1-2.130.26062220.19614522X-RAY DIFFRACTION93.35
2.13-2.160.30431760.19964635X-RAY DIFFRACTION94.22
2.16-2.20.25112500.18914509X-RAY DIFFRACTION93.63
2.2-2.230.27042700.19384529X-RAY DIFFRACTION94.38
2.23-2.270.25352360.18744605X-RAY DIFFRACTION94.18
2.27-2.320.23842340.18434574X-RAY DIFFRACTION95.13
2.32-2.360.26582730.18854556X-RAY DIFFRACTION94.5
2.36-2.420.26442470.18744606X-RAY DIFFRACTION94.8
2.42-2.470.2652290.19014660X-RAY DIFFRACTION96.16
2.47-2.530.25362380.19564668X-RAY DIFFRACTION95.78
2.53-2.60.26012250.19084696X-RAY DIFFRACTION96.13
2.6-2.680.24592540.19174658X-RAY DIFFRACTION96.16
2.68-2.770.2312250.1894684X-RAY DIFFRACTION96.6
2.77-2.860.2392780.18584674X-RAY DIFFRACTION96.96
2.86-2.980.27032440.19014731X-RAY DIFFRACTION97.22
2.98-3.110.22812210.18164764X-RAY DIFFRACTION96.97
3.11-3.280.22312230.17414726X-RAY DIFFRACTION96.87
3.28-3.480.23492650.16644650X-RAY DIFFRACTION96.17
3.48-3.750.20522350.15644663X-RAY DIFFRACTION95.44
3.75-4.130.16722530.1464627X-RAY DIFFRACTION95.09
4.13-4.730.17392350.13624565X-RAY DIFFRACTION92.81
4.73-5.950.18962630.15654510X-RAY DIFFRACTION92.45
5.96-45.80.18862380.17664253X-RAY DIFFRACTION85.12
Refinement TLS params.Method: refined / Origin x: 36.8702297669 Å / Origin y: 2.82267561556 Å / Origin z: 17.9769695564 Å
111213212223313233
T0.194184139553 Å2-0.000522107895468 Å2-0.00700378492928 Å2-0.190769269457 Å20.00305624271796 Å2--0.182334111234 Å2
L0.346333134134 °2-0.0430176179538 °20.0371153972373 °2-0.286320037166 °2-0.00287754664736 °2--0.162226874216 °2
S0.00649099938651 Å °0.00486427429311 Å °0.0352708601524 Å °-0.00291007549863 Å °-0.00277338676719 Å °-0.026051912978 Å °-0.0102652363095 Å °0.0111486578782 Å °-0.00259226704353 Å °
Refinement TLS groupSelection details: all

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