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- PDB-4c9c: Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-1... -

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Basic information

Entry
Database: PDB / ID: 4c9c
TitleCrystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 1E protein (Form A)
ComponentsMAJOR STRAWBERRY ALLERGEN FRA A 1-E
KeywordsALLERGEN / START / PYR/PYL/RCAR / BET V 1
Function / homology
Function and homology information


flavonoid binding / flavonoid biosynthetic process / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
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-E
Similarity search - Component
Biological speciesFRAGARIA X ANANASSA (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCasanal, A. / Zander, U. / Valpuesta, V. / Marquez, J.A.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: The Strawberry Pathogenesis-Related 10 (Pr-10) Fra a Proteins Control Flavonoid Biosynthesis by Binding to Metabolic Intermediates.
Authors: Casanal, A. / Zander, U. / Munoz, C. / Dupeux, F. / Luque, I. / Botella, M.A. / Schwab, W. / Valpuesta, V. / Marquez, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Purification, Crystallization and Preliminary X-Ray Analysis of the Strawberry Allergens Fra a 1E and Fra a 3 in the Presence of Catechin.
Authors: Casanal, A. / Zander, U. / Dupeux, F. / Valpuesta, V. / Marquez, J.A.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR STRAWBERRY ALLERGEN FRA A 1-E
B: MAJOR STRAWBERRY ALLERGEN FRA A 1-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2516
Polymers35,8752
Non-polymers3764
Water2,828157
1
A: MAJOR STRAWBERRY ALLERGEN FRA A 1-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0332
Polymers17,9371
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MAJOR STRAWBERRY ALLERGEN FRA A 1-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2184
Polymers17,9371
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.020, 74.420, 84.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99, -0.1409, -0.0057), (-0.1408, -0.99, 0.0116), (-0.0073, -0.0107, -0.9999)
Vector: 0.487, 1.6706, 73.0921)

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Components

#1: Protein MAJOR STRAWBERRY ALLERGEN FRA A 1-E / FRA A 1E


Mass: 17937.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FRAGARIA X ANANASSA (strawberry) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q256S2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.2→36.03 Å / Num. obs: 24107 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 14
Reflection shellResolution: 2.2→36.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E85

3e85


Resolution: 2.2→36.03 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.454 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25011 1142 5 %RANDOM
Rwork0.20563 ---
obs0.20788 21722 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.955 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 22 157 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192501
X-RAY DIFFRACTIONr_bond_other_d0.0050.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9753379
X-RAY DIFFRACTIONr_angle_other_deg0.90135525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00825.36197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97115430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 82 -
Rwork0.223 1563 -
obs--100 %

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