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- PDB-1z3q: Resolution of the structure of the allergenic and antifungal bana... -

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Basic information

Entry
Database: PDB / ID: 1z3q
TitleResolution of the structure of the allergenic and antifungal banana fruit thaumatin-like protein at 1.7A
ComponentsThaumatin-like Protein
KeywordsANTIFUNGAL PROTEIN / beta sandwich
Function / homology
Function and homology information


cytoplasmic vesicle
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
Ripening-associated protein
Similarity search - Component
Biological speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLeone, P. / Menu-Bouaouiche, L. / Peumans, W.J. / Barre, A. / Payan, F. / Roussel, A. / Van Damme, E.J.M. / Rouge, P.
CitationJournal: Biochimie / Year: 2006
Title: Resolution of the structure of the allergenic and antifungal banana fruit thaumatin-like protein at 1.7-A
Authors: Leone, P. / Menu-Bouaouiche, L. / Peumans, W.J. / Payan, F. / Barre, A. / Roussel, A. / Van Damme, E.J.M. / Rouge, P.
History
DepositionMar 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4324
Polymers21,2461
Non-polymers1863
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.844, 52.839, 80.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thaumatin-like Protein


Mass: 21245.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Musa acuminata (dwarf banana) / Tissue: pulp / References: UniProt: O22322
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.3 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Ammonium Sulfate, Sodium Acatate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→42.2 Å / Num. all: 20728 / Num. obs: 20095 / % possible obs: 96.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 15.31 Å2 / Rsym value: 0.042 / Net I/σ(I): 17.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 9.4 / Num. unique all: 1920 / Rsym value: 0.131 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1THV

1thv


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.547 / SU ML: 0.053 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17712 1027 5.1 %RANDOM
Rwork0.14248 ---
all0.14426 20728 --
obs0.14426 20067 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 12 247 1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211539
X-RAY DIFFRACTIONr_bond_other_d0.0020.021254
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9332093
X-RAY DIFFRACTIONr_angle_other_deg0.80832930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255199
X-RAY DIFFRACTIONr_chiral_restr0.0830.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined0.2040.2272
X-RAY DIFFRACTIONr_nbd_other0.2510.21531
X-RAY DIFFRACTIONr_nbtor_other0.0820.2875
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.218
X-RAY DIFFRACTIONr_mcbond_it0.611.5986
X-RAY DIFFRACTIONr_mcangle_it1.12521576
X-RAY DIFFRACTIONr_scbond_it1.9253553
X-RAY DIFFRACTIONr_scangle_it3.0844.5517
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.242 75
Rwork0.177 1311
obs-1027

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