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

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Basic information

Entry
Database: PDB / ID: 4mbt
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: 1.65 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
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water2,810156
1
A: VVTL1


Theoretical massNumber of molelcules
Total (without water)21,3021
Polymers21,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
Unit cell
Length a, b, c (Å)122.560, 52.600, 91.610
Angle α, β, γ (deg.)90.00, 130.02, 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.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.58 M Mg acetate, 0.2 M MES, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→23.46 Å / Num. all: 55152 / Num. obs: 53130 / % possible obs: 90.2 % / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.692.40.4111.8194.3
1.7-1.792.40.2513193.1
1.8-1.912.40.1784.2192.3
1.92-2.072.50.1236191.6
2.08-2.262.50.0887.3190.1
2.27-2.532.50.079.7188.7
2.54-2.922.60.0659.3186.6
2.93-3.582.50.0578.6185
3.59-5.052.60.0519.6184.6
5.06-23.462.80.068181.2

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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 4L5H

4l5h


Resolution: 1.65→8.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.083 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25687 2457 5.1 %RANDOM
Rwork0.22356 ---
obs0.22525 45549 88.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.138 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→8.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 6 156 3134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.023159
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2841.954334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.94724.964139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5811514
X-RAY DIFFRACTIONr_chiral_restr0.1640.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212522
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.65→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 203 -
Rwork0.315 3307 -
obs--93.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0554-0.0142-0.00270.01550.00840.00720.00050.0059-00.0034-0.00670.00350.0017-0.00040.00620.003-0.0016-0.00120.00550.00470.012920.1544-0.2458-0.1424
20.0112-0.00610.00250.00960.01780.06370.00390.00080.0052-0.0006-0.005-0.00350.0034-0.00740.00120.0062-0.0038-0.00110.00540.00150.0099-0.715922.662624.7912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 222
2X-RAY DIFFRACTION2B25 - 222

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