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- PDB-4l5h: Structure of haze forming proteins in white wines: Vitis vinifera... -

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Basic information

Entry
Database: PDB / ID: 4l5h
TitleStructure of haze forming proteins in white wines: Vitis vinifera thaumatin-like proteins
ComponentsVVTL1
KeywordsANTIFUNGAL PROTEIN / PLANT PROTEIN
Function / homology
Function and homology information


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
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMarangon, M. / Menz, R.I. / Waters, E.J. / Van Sluyter, S.C.
CitationJournal: Plos One / Year: 2014
Title: Structure of Haze Forming Proteins in White Wines: Vitis vinifera Thaumatin-Like Proteins.
Authors: Marangon, M. / Van Sluyter, S.C. / Waters, E.J. / Menz, R.I.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJul 3, 2013ID: 4H8T
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Sep 20, 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 1.3Nov 27, 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: VVTL1
B: VVTL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6953
Polymers42,6032
Non-polymers921
Water3,261181
1
A: VVTL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3942
Polymers21,3021
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VVTL1


Theoretical massNumber of molelcules
Total (without water)21,3021
Polymers21,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.210, 52.730, 94.390
Angle α, β, γ (deg.)90.00, 132.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VVTL1


Mass: 21301.609 Da / Num. of mol.: 2 / Fragment: UNP residues 25-222 / Source method: isolated from a natural source / Details: Grape juice / Source: (natural) Vitis vinifera (wine grape) / Strain: Sauvignon Blanc / References: UniProt: O04708
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Na Acetate pH 4.6, 2 M Mg acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956639 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956639 Å / Relative weight: 1
ReflectionResolution: 1.59→12.63 Å / Num. obs: 29314 / % possible obs: 75.7 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.59-1.670.4271.84990178.2
1.68-1.770.2852.74748177.5
1.78-1.890.2013.94371176.9
1.9-2.040.1365.74068176.9
2.05-2.240.0997.73772176.5
2.25-2.50.0789.43382175.7
2.51-2.890.06311.12961174.5
2.9-3.550.04414.52498173.1
3.56-5.020.03815.31905170.4
5.03-12.630.04412.4936161.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JRU

4jru


Resolution: 1.8→12.63 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.176 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23286 1596 5.2 %RANDOM
Rwork0.19811 ---
obs0.19992 29314 74.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.485 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→12.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 6 181 3159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.023144
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9524304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2525410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.1124.783138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85115458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3081515
X-RAY DIFFRACTIONr_chiral_restr0.1620.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212495
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 108 -
Rwork0.22 2133 -
obs--76.62 %
Refinement TLS params.Method: refined / Origin x: -28.6775 Å / Origin y: 0.7956 Å / Origin z: -10.2748 Å
111213212223313233
T0.0219 Å2-0.0179 Å20.0063 Å2-0.0231 Å2-0.0029 Å2--0.0226 Å2
L0.5153 °2-0.1774 °20.1338 °2-0.6806 °2-0.1595 °2--0.781 °2
S0.0314 Å °0.0091 Å °-0.0088 Å °-0.0306 Å °-0.0433 Å °-0.0236 Å °-0.0173 Å °0.0444 Å °0.0119 Å °

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