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- PDB-4c94: Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-1... -

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Basic information

Entry
Database: PDB / ID: 4c94
TitleCrystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 3 protein in complex with Catechin
ComponentsFRA A 3 ALLERGEN
KeywordsALLERGEN / PYR/PYL/RCAR / BET V 1 / FLAVONOIDS
Function / homology
Function and homology information


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
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
Chem-KXN / Major strawberry allergen Fra a 1-3
Similarity search - Component
Biological speciesFRAGARIA X ANANASSA (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.3Nov 6, 2013Group: Atomic model
Revision 1.4Dec 25, 2013Group: Database references
Revision 1.5Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.6Dec 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

Downloads & links

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Assembly

Deposited unit
A: FRA A 3 ALLERGEN
B: FRA A 3 ALLERGEN
C: FRA A 3 ALLERGEN
D: FRA A 3 ALLERGEN
E: FRA A 3 ALLERGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,82711
Polymers88,0855
Non-polymers1,7426
Water21612
1
A: FRA A 3 ALLERGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9072
Polymers17,6171
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FRA A 3 ALLERGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9072
Polymers17,6171
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FRA A 3 ALLERGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9072
Polymers17,6171
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FRA A 3 ALLERGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9072
Polymers17,6171
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FRA A 3 ALLERGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1983
Polymers17,6171
Non-polymers5812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.899, 206.594, 174.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1256, -0.6761, 0.7261), (-0.4711, -0.6035, -0.6434), (0.8731, -0.4228, -0.2427)-78.6649, -64.187, 37.3457
2given(-0.9811, -0.087, -0.1726), (-0.1593, -0.1422, 0.9769), (-0.1096, 0.986, 0.1257)-65.2411, -63.5337, 46.9167
3given(0.1183, 0.7905, -0.6009), (0.5142, -0.5664, -0.644), (-0.8495, -0.2328, -0.4735)4.8426, -28.8309, -7.7572
4given(-0.9767, 0.1486, -0.1548), (0.1794, 0.1696, -0.969), (-0.1177, -0.9742, -0.1923)-52.893, 64.9342, -47.9655

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Components

#1: Protein
FRA A 3 ALLERGEN


Mass: 17616.994 Da / Num. of mol.: 5
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: D0E0C7
#2: Chemical
ChemComp-KXN / (2R,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol


Mass: 290.268 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H14O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 7.09 Å3/Da / Density % sol: 82.66 % / Description: NONE
Crystal growpH: 7 / Details: 2.25 M SODIUM MALONATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 49904 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.7
Reflection shellResolution: 3→30 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 4C9C

4c9c


Resolution: 3→29.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.271 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19933 2536 5.1 %RANDOM
Rwork0.17751 ---
obs0.17861 47343 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 3→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 126 12 6318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0196446
X-RAY DIFFRACTIONr_bond_other_d0.0070.026178
X-RAY DIFFRACTIONr_angle_refined_deg2.5731.9938701
X-RAY DIFFRACTIONr_angle_other_deg1.573.00414361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7695794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95425.564257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.831151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.938155
X-RAY DIFFRACTIONr_chiral_restr0.140.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217121
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021310
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: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 197 -
Rwork0.295 3447 -
obs--100 %

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