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- PDB-5xty: Crystal Structure of 11S allergen from Cocos nucifera L. -

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Basic information

Entry
Database: PDB / ID: 5xty
TitleCrystal Structure of 11S allergen from Cocos nucifera L.
Components11S globulin isoform 1
KeywordsALLERGEN / 11S Allergen / cocosin / coconut / twinning
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 / Resolution: 2.2 Å
AuthorsVajravijayan, S. / Nandhagopal, N. / Gunasekaran, K.
CitationJournal: Mol. Immunol. / Year: 2017
Title: Crystal structure determination and analysis of 11S coconut allergen: Cocosin
Authors: Vajravijayan, S. / Nandhagopal, N. / Gunasekaran, K.
History
DepositionJun 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)105,3332
Polymers105,3332
Non-polymers00
Water2,810156
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)315,9986
Polymers315,9986
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area40900 Å2
ΔGint-204 kcal/mol
Surface area80600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.056, 92.056, 212.309
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: 52666.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cocos nucifera (coconut palm) / References: UniProt: A0A0R7UCU5, UniProt: A0A222NNM9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
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: 1.64 Å3/Da / Density % sol: 25.16 % / Description: Prismatic crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 0.2M Mgcl2 and 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.53
ReflectionResolution: 2.2→31.7 Å / Num. obs: 33993 / % possible obs: 99.7 % / Redundancy: 2.5 % / Rsym value: 0.082 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3338 / % possible all: 97.45

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSJune 1, 2017data reduction
SCALAdata scaling
BALBES1.1.5phasing
RefinementResolution: 2.2→29.833 Å / Cross valid method: FREE R-VALUE / σ(F): 41.51 / Phase error: 35.4 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2991 1709 5.03 %
Rwork0.1991 --
obs0.2202 33978 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 0 156 5768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015712
X-RAY DIFFRACTIONf_angle_d1.0997703
X-RAY DIFFRACTIONf_dihedral_angle_d9.9464160
X-RAY DIFFRACTIONf_chiral_restr0.053847
X-RAY DIFFRACTIONf_plane_restr0.0061025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2009-2.26560.34041660.32542600X-RAY DIFFRACTION91
2.2656-2.33860.32531080.34842720X-RAY DIFFRACTION96
2.3386-2.42210.36511650.32762673X-RAY DIFFRACTION94
2.4221-2.51890.35171310.35162685X-RAY DIFFRACTION95
2.5189-2.63340.39231740.34212656X-RAY DIFFRACTION94
2.6334-2.7720.39771530.32552696X-RAY DIFFRACTION95
2.772-2.94520.35231280.30612679X-RAY DIFFRACTION95
2.9452-3.1720.33551760.29062673X-RAY DIFFRACTION94
3.172-3.490.34171330.25062686X-RAY DIFFRACTION95
3.49-3.99230.33761090.19782760X-RAY DIFFRACTION96
3.9923-5.01950.25481390.13352663X-RAY DIFFRACTION95
5.0195-21.64760.27411240.14272724X-RAY DIFFRACTION96

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