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- PDB-5wpw: Crystal structure of coconut allergen cocosin -

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Basic information

Entry
Database: PDB / ID: 5wpw
TitleCrystal structure of coconut allergen cocosin
Components11S globulin isoform 1
KeywordsALLERGEN / 11S globulin / seed storage protein
Function / homology
Function and homology information


seed maturation / extraorganismal space / seed development / nutrient reservoir activity
Similarity search - Function
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
Cocosin 1 / Cocosin 1
Similarity search - Component
Biological speciesCocos nucifera (coconut palm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.847 Å
AuthorsJin, T. / Zhang, Y.
CitationJournal: J. Agric. Food Chem. / Year: 2017
Title: Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera)
Authors: Jin, T. / Wang, C. / Zhang, C. / Wang, Y. / Chen, Y.W. / Guo, F. / Howard, A. / Cao, M.J. / Fu, T.J. / McHugh, T.H. / Zhang, Y.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 11S globulin isoform 1
B: 11S globulin isoform 1


Theoretical massNumber of molelcules
Total (without water)96,3572
Polymers96,3572
Non-polymers00
Water3,855214
1
A: 11S globulin isoform 1
B: 11S globulin isoform 1

A: 11S globulin isoform 1
B: 11S globulin isoform 1

A: 11S globulin isoform 1
B: 11S globulin isoform 1


Theoretical massNumber of molelcules
Total (without water)289,0706
Polymers289,0706
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area46220 Å2
ΔGint-214 kcal/mol
Surface area64370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.410, 92.410, 212.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 11S globulin isoform 1


Mass: 48178.266 Da / Num. of mol.: 2 / Fragment: UNP residues 43-466 / Mutation: A398E, V416I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cocos nucifera (coconut palm) / Gene: COS-1 / Production host: Cocos nucifera (coconut palm) / References: UniProt: A0A0R7UCU5, UniProt: A0A222NNM9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.66 Å3/Da / Density % sol: 32.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.7M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.847→50 Å / Num. obs: 55347 / % possible obs: 95.1 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 12.2
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.05 / CC1/2: 0.869 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3V

3c3v


Resolution: 1.847→29.947 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 36.32
RfactorNum. reflection% reflection
Rfree0.2917 2807 5.08 %
Rwork0.2289 --
obs0.2321 55270 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.847→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 0 214 6181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086053
X-RAY DIFFRACTIONf_angle_d0.948165
X-RAY DIFFRACTIONf_dihedral_angle_d10.2613705
X-RAY DIFFRACTIONf_chiral_restr0.059902
X-RAY DIFFRACTIONf_plane_restr0.0051090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.847-1.87890.82081280.80062263X-RAY DIFFRACTION82
1.8789-1.9130.56271340.42212669X-RAY DIFFRACTION97
1.913-1.94980.40771570.34592692X-RAY DIFFRACTION98
1.9498-1.98960.42281450.35472650X-RAY DIFFRACTION96
1.9896-2.03280.4211490.32692671X-RAY DIFFRACTION97
2.0328-2.08010.37141350.32222634X-RAY DIFFRACTION95
2.0801-2.13210.40911290.30642680X-RAY DIFFRACTION97
2.1321-2.18980.38561470.322603X-RAY DIFFRACTION95
2.1898-2.25420.38011300.29752664X-RAY DIFFRACTION95
2.2542-2.32690.34641270.30032575X-RAY DIFFRACTION94
2.3269-2.410.38831390.28582588X-RAY DIFFRACTION94
2.41-2.50650.30991460.27152574X-RAY DIFFRACTION94
2.5065-2.62050.33861190.27672658X-RAY DIFFRACTION95
2.6205-2.75860.30191420.25792604X-RAY DIFFRACTION95
2.7586-2.93130.26251650.24492635X-RAY DIFFRACTION96
2.9313-3.15740.29651290.23172642X-RAY DIFFRACTION95
3.1574-3.47470.2531640.20732596X-RAY DIFFRACTION95
3.4747-3.97650.30561380.18682685X-RAY DIFFRACTION97
3.9765-5.00610.21711460.15352721X-RAY DIFFRACTION98
5.0061-29.95130.21351380.18032659X-RAY DIFFRACTION96

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