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- PDB-2ahn: High resolution structure of a cherry allergen Pru av 2 -

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Basic information

Entry
Database: PDB / ID: 2ahn
TitleHigh resolution structure of a cherry allergen Pru av 2
ComponentsThaumatin-like protein
KeywordsALLERGEN / Thaumatin-like protein
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / IgE binding / extracellular region
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glucan endo-1,3-beta-glucosidase
Similarity search - Component
Biological speciesPrunus avium (sweet cherry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDall'Antonia, Y. / Pavkov, T. / Fuchs, H. / Breiteneder, H. / Keller, W.
Citation
Journal: To be published
Title: The high-resolution crystal structure of an allergenic thaumatin-like protein, Pru av 2, isolated from ripe cherries
Authors: Dall'Antonia, Y. / Pavkov, T. / Fuchs, H. / Breiteneder, H. / Keller, W.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005
Title: Crystallization and preliminary structure determination of the plant food allergen Pru av 2
Authors: Dall'Antonia, Y. / Pavkov, T. / Fuchs, H. / Breiteneder, H. / Keller, W.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin-like protein


Theoretical massNumber of molelcules
Total (without water)23,3481
Polymers23,3481
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.288, 41.150, 58.946
Angle α, β, γ (deg.)90.00, 107.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thaumatin-like protein


Mass: 23347.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Prunus avium (sweet cherry) / References: UniProt: P50694
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.1 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 3.5
Details: PEG 3350, citric acid, pH 3.5, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1.3→16.69 Å / Num. obs: 49825 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Χ2: 1.417 / Net I/σ(I): 28.6
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 9.8 / Num. measured obs: 2457 / Χ2: 1.489 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.554 / Cor.coef. Fo:Fc: 0.234
Highest resolutionLowest resolution
Rotation3 Å39.96 Å
Translation3 Å39.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
SHELXrefinement
PDB_EXTRACT1.7data extraction
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THV

1thv


Resolution: 1.3→16.69 Å / Num. parameters: 17049 / Num. restraintsaints: 21079 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.146 2223 -RANDOM
Rwork0.117 ---
obs0.117 36754 85.6 %-
all-42877 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 14.535 Å2
Refinement stepCycle: LAST / Resolution: 1.3→16.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 0 235 1865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.033
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.07
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.083

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