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- PDB-4bct: Crystal structure of kiwi-fruit allergen Act d 2 -

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Basic information

Entry
Database: PDB / ID: 4bct
TitleCrystal structure of kiwi-fruit allergen Act d 2
ComponentsTHAUMATIN-LIKE PROTEIN
KeywordsALLERGEN / TLP
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / 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
Thaumatin-like protein
Similarity search - Component
Biological speciesACTINIDIA DELICIOSA (kiwifruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.98 Å
AuthorsPavkov-Keller, T. / Bublin, M. / Jankovic, M. / Breiteneder, H. / Keller, W.
CitationJournal: To be Published
Title: Crystal Structure of Kiwi-Fruit Allergen Act D 2
Authors: Pavkov-Keller, T. / Bublin, M. / Jankovic, M. / Breiteneder, H. / Keller, W.
History
DepositionOct 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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: THAUMATIN-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8692
Polymers21,6311
Non-polymers2381
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.541, 48.312, 50.580
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THAUMATIN-LIKE PROTEIN / ACT D 2 / ALLERGEN ACT D 2


Mass: 21631.193 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-225 / Source method: isolated from a natural source / Source: (natural) ACTINIDIA DELICIOSA (kiwifruit) / References: UniProt: P81370
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1.98 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growDetails: 22-30% PEG 6000, PH 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 97776 / % possible obs: 99 % / Observed criterion σ(I): 2.5 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 0.98→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.398 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES - REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.13125 4842 5 %RANDOM
Rwork0.11315 ---
obs0.11406 91955 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 0.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 15 339 1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3941.9522351
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8724.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.82715247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3461510
X-RAY DIFFRACTIONr_chiral_restr0.1330.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211396
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_it1.9731.51064
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.94921727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6283646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5464.5619
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.27631710
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.98→1.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 339 -
Rwork0.222 6673 -
obs--98.15 %

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