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- PDB-5amw: Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-1... -

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Basic information

Entry
Database: PDB / ID: 5amw
TitleCrystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 2 protein (A141F) processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsFra a 2 allergen
KeywordsALLERGEN / PYR/PYL/RCAR / BET V 1 / FLAVONOIDS / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO-COOLING / CRYSTALDIRECT
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
Major strawberry allergen Fra a 1-2
Similarity search - Component
Biological speciesFragaria ananassa (strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsZander, U. / Casanal, A. / Pott, D. / Valpuesta, V. / Hoffmann, G. / Cornaciu, I. / Cipriani, F. / Marquez, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation.
Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A.
History
DepositionSep 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Data collection / Database references
Revision 1.2May 11, 2016Group: Data collection
Revision 1.3Dec 5, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fra a 2 allergen
B: Fra a 2 allergen


Theoretical massNumber of molelcules
Total (without water)35,4782
Polymers35,4782
Non-polymers00
Water3,279182
1
A: Fra a 2 allergen


Theoretical massNumber of molelcules
Total (without water)17,7391
Polymers17,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fra a 2 allergen


Theoretical massNumber of molelcules
Total (without water)17,7391
Polymers17,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.559, 41.463, 92.058
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2541, 0.0207, 0.967), (-0.0283, -0.9995, 0.014), (0.9668, -0.0238, 0.2545)
Vector: -13.7973, 18.5001, 10.7018)

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Components

#1: Protein Fra a 2 allergen


Mass: 17739.070 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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS,PH=5.5, 0.2 M AMMONIUM SULFATE, 25% PEG 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9763
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 28520 / % possible obs: 99.9 % / Observed criterion σ(I): 2.2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: REFMAC / Version: 5.8.0123 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.868 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26493 1441 5.1 %RANDOM
Rwork0.22097 ---
obs0.22319 27078 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.023 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20.06 Å2
2--1.05 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 0 182 2680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192548
X-RAY DIFFRACTIONr_bond_other_d0.0060.022434
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9723434
X-RAY DIFFRACTIONr_angle_other_deg1.02135666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66725.769104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.964152
X-RAY DIFFRACTIONr_chiral_restr0.110.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
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_it2.9483.1581294
X-RAY DIFFRACTIONr_mcbond_other2.943.1561293
X-RAY DIFFRACTIONr_mcangle_it3.8444.7141614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3993.6911254
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 111 -
Rwork0.297 1985 -
obs--100 %

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