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- PDB-6st8: Crystal structure of the strawberry pathogenesis-related 10 (PR-1... -

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Basic information

Entry
Database: PDB / ID: 6st8
TitleCrystal structure of the strawberry pathogenesis-related 10 (PR-10) Fra a 1.02 protein
ComponentsMajor strawberry allergen Fra a 1-2
KeywordsALLERGEN / Fragaria x ananassa / Fra a 1 / fruit / ripening / PR-10
Function / homology
Function and homology information


flavonoid biosynthetic process / response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major strawberry allergen Fra a 1-2
Similarity search - Component
Biological speciesFragaria ananassa (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsOrozco-Navarrete, B. / Kaczmarska, Z. / Dupeux, F. / Pott, D. / Diaz Perales, A. / Casanal, A. / Marquez, J.A. / Valpuesta, V. / Merchante, C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBIO2013-33199-R Spain
Ministry of Economy and CompetitivenessBES-2014-068723 Spain
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: Structural Bases for the Allergenicity of Fra a 1.02 in Strawberry Fruits.
Authors: Orozco-Navarrete, B. / Kaczmarska, Z. / Dupeux, F. / Garrido-Arandia, M. / Pott, D. / Perales, A.D. / Casanal, A. / Marquez, J.A. / Valpuesta, V. / Merchante, C.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Major strawberry allergen Fra a 1-2
B: Major strawberry allergen Fra a 1-2


Theoretical massNumber of molelcules
Total (without water)35,4402
Polymers35,4402
Non-polymers00
Water3,261181
1
A: Major strawberry allergen Fra a 1-2


Theoretical massNumber of molelcules
Total (without water)17,7201
Polymers17,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major strawberry allergen Fra a 1-2


Theoretical massNumber of molelcules
Total (without water)17,7201
Polymers17,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.92, 41.73, 91.35
Angle α, β, γ (deg.)90, 117.14, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-254-

HOH

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Components

#1: Protein Major strawberry allergen Fra a 1-2 / Class 10 plant pathogenesis-related protein Fra a 1.02 / PR10-related protein Fra a 1.02


Mass: 17720.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fragaria ananassa (strawberry) / Gene: FRAA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0E0C6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis-Tris pH5.5 140mM Ammonium Sulfate 33% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072274 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072274 Å / Relative weight: 1
ReflectionResolution: 2.04→52.45 Å / Num. obs: 15170 / % possible obs: 88.1 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.047 / Rrim(I) all: 0.085 / Net I/σ(I): 8.7
Reflection shellResolution: 2.04→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 760 / CC1/2: 0.56 / Rpim(I) all: 0.541 / Rrim(I) all: 0.957 / % possible all: 49.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AMW

5amw


Resolution: 2.04→47.13 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.41 / SU Rfree Blow DPI: 0.275 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.278 791 -RANDOM
Rwork0.212 ---
obs0.216 15169 65.7 %-
Displacement parametersBiso mean: 50.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.913 Å20 Å20.0203 Å2
2--0.7342 Å20 Å2
3---0.1789 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.04→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 0 181 2656
LS refinement shellResolution: 2.04→2.21 Å
RfactorNum. reflection% reflection
Rfree0.1833 25 -
Rwork0.2085 --
obs0.2068 389 7.81 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-5.58640.066230.246
217.077117.975112.9593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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