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- PDB-5e1r: Crystal structure of pecan (carya illinoinensis) vicilin, a new f... -

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Basic information

Entry
Database: PDB / ID: 5e1r
TitleCrystal structure of pecan (carya illinoinensis) vicilin, a new food allergen
Components7S vicilin
KeywordsALLERGEN / vicilin / food allergy
Function / homology
Function and homology information


seed maturation / seed development / nutrient reservoir activity / protein homotrimerization / copper ion binding
Similarity search - Function
Vicilin, N-terminal / Vicilin N terminal region / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...Vicilin, N-terminal / Vicilin N terminal region / : / 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
COPPER (II) ION / Vicilin Car i 2.0101
Similarity search - Component
Biological speciesCarya illinoinensis (pecan)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsZhang, Y.Z.
CitationJournal: J.Agric.Food Chem. / Year: 2016
Title: Identification and Characterization of a New Pecan [Carya illinoinensis (Wangenh.) K. Koch] Allergen, Car i 2.
Authors: Zhang, Y. / Lee, B. / Du, W.X. / Lyu, S.C. / Nadeau, K.C. / Grauke, L.J. / Zhang, Y. / Wang, S. / Fan, Y. / Yi, J. / McHugh, T.H.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7S vicilin
B: 7S vicilin
C: 7S vicilin
D: 7S vicilin
E: 7S vicilin
F: 7S vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,71218
Polymers294,6226
Non-polymers1,09012
Water72140
1
A: 7S vicilin
B: 7S vicilin
C: 7S vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8569
Polymers147,3113
Non-polymers5456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15950 Å2
ΔGint-128 kcal/mol
Surface area37380 Å2
MethodPISA
2
D: 7S vicilin
E: 7S vicilin
F: 7S vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8569
Polymers147,3113
Non-polymers5456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-128 kcal/mol
Surface area38180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.691, 151.610, 342.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
7S vicilin


Mass: 49103.621 Da / Num. of mol.: 6 / Fragment: UNP residues 369-792
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carya illinoinensis (pecan) / Gene: pec2a1a, pec3a1a, pec4a1a / Plasmid: pTAP1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3STU4
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.88 Å3/Da / Density % sol: 34.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.1M Sodium cacodylat trihydrate 30%(v/v) MPD

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationMonochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 61694 / % possible obs: 92.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.2 / Χ2: 0.996 / Net I/av σ(I): 7.364 / Net I/σ(I): 9.3 / Num. measured all: 422187
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.65-2.72.30.49519391.00158.5
2.7-2.742.50.50421721.00267.8
2.74-2.82.90.48824560.99675.6
2.8-2.853.30.4822634179.4
2.85-2.923.70.4428161.00587.4
2.92-2.984.20.42829870.99191.6
2.98-3.064.70.38131121.00993.2
3.06-3.145.10.37632071.00898.6
3.14-3.235.80.37332481.0199.9
3.23-3.346.40.35133381.01199.4
3.34-3.467.20.34232501.005100
3.46-3.67.40.32433551.009100
3.6-3.767.60.29132540.988100
3.76-3.967.90.26133661.015100
3.96-4.218.10.21633150.977100
4.21-4.538.40.19933121.003100
4.53-4.998.70.18533890.981100
4.99-5.719.40.18233880.977100
5.71-7.1911.20.19134981.017100
7.19-5013.10.1536580.972100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→46.598 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 1998 3.38 %
Rwork0.2178 57080 -
obs0.2193 59078 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.31 Å2 / Biso mean: 18.3902 Å2 / Biso min: 0.05 Å2
Refinement stepCycle: final / Resolution: 2.651→46.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16980 0 54 40 17074
Biso mean--15.74 14.1 -
Num. residues----2143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417352
X-RAY DIFFRACTIONf_angle_d0.79523463
X-RAY DIFFRACTIONf_chiral_restr0.0312543
X-RAY DIFFRACTIONf_plane_restr0.0043144
X-RAY DIFFRACTIONf_dihedral_angle_d15.2346471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6508-2.71710.3248710.27192012208345
2.7171-2.79050.3589940.2832717281161
2.7905-2.87260.29961100.27773139324969
2.8726-2.96530.34841250.28183572369780
2.9653-3.07130.32851430.27074103424690
3.0713-3.19420.29771570.26424476463399
3.1942-3.33960.33321580.250745274685100
3.3396-3.51560.27291590.236145524711100
3.5156-3.73570.31071590.235145414700100
3.7357-4.0240.26181610.218445714732100
4.024-4.42870.20311600.181145854745100
4.4287-5.06890.24151620.173246404802100
5.0689-6.38360.22321660.206247064872100
6.3836-46.60570.2221730.191249395112100

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