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- PDB-4l5h: Structure of haze forming proteins in white wines: Vitis vinifera... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l5h | |||||||||
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Title | Structure of haze forming proteins in white wines: Vitis vinifera thaumatin-like proteins | |||||||||
![]() | VVTL1 | |||||||||
![]() | ANTIFUNGAL PROTEIN / PLANT PROTEIN | |||||||||
Function / homology | ![]() 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 species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Marangon, M. / Menz, R.I. / Waters, E.J. / Van Sluyter, S.C. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.2 KB | Display | ![]() |
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PDB format | ![]() | 126.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.3 KB | Display | ![]() |
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Full document | ![]() | 436.1 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jruSC ![]() 4mbtC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | 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) ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.956639 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.485 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→12.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -28.6775 Å / Origin y: 0.7956 Å / Origin z: -10.2748 Å
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