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- PDB-3zs3: High resolution structure of Mal d 2, the thaumatin like food all... -

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Basic information

Entry
Database: PDB / ID: 3zs3
TitleHigh resolution structure of Mal d 2, the thaumatin like food allergen from apple
ComponentsTHAUMATIN-LIKE PROTEIN
KeywordsALLERGEN
Function / homology
Function and homology information


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
ACETATE ION / ACETIC ACID / FORMIC ACID / SUCCINIC ACID / Thaumatin-like protein / Thaumatin-like protein 1a
Similarity search - Component
Biological speciesMALUS X DOMESTICA (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKopec, J. / Smole, U. / Pavkov, T. / Breiteneder, H. / Keller, W.
CitationJournal: To be Published
Title: High Resolution Structure of Mal D 2, the Thaumatin Like Food Allergen from Apple
Authors: Kopec, J. / Smole, U. / Pavkov, T. / Breiteneder, H. / Keller, W.
History
DepositionJun 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THAUMATIN-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,77810
Polymers23,2261
Non-polymers5529
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.662, 54.060, 45.239
Angle α, β, γ (deg.)90.00, 113.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THAUMATIN-LIKE PROTEIN / MALD2


Mass: 23225.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MALUS X DOMESTICA (apple) / Organ: FRUIT / References: UniProt: Q3BCT8, UniProt: Q9FSG7*PLUS

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Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.75 % / Description: NONE
Crystal growDetails: 60% TACSIMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→54.06 Å / Num. obs: 16738 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 12.741 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHN

2ahn


Resolution: 1.8→41.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18757 846 5.1 %RANDOM
Rwork0.14892 ---
obs0.15081 15877 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.4 Å2
2--0.45 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 37 145 1803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9752345
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83725.55663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13715239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.305154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221345
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6311.51141
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20721824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1953575
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8194.5518
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 58 -
Rwork0.183 1147 -
obs--99.42 %

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