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Yorodumi- PDB-2wbz: 1.6 A Structure of Thaumatin Crystallized without Tartrate at 4 C -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wbz | ||||||
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Title | 1.6 A Structure of Thaumatin Crystallized without Tartrate at 4 C | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / TASTE-MODIFYING PROTEIN / KINETICS OF CRYSTALLIZATION / SWEET PROTEIN / DISULFIDE BOND / THAUMATIN / CHIRALITY / MICROBATCH / TEMPERATURE / CYTOPLASMIC VESICLE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jakoncic, J. / Asherie, N. / Ginsberg, C. | ||||||
Citation | Journal: Cryst.Growth Des. / Year: 2009 Title: Tartrate Chirality Determines Thaumatin Crystal Habit Authors: Asherie, N. / Jakoncic, J. / Ginsberg, C. / Greenbaum, A. / Stojanoff, V. / Hrnjez, B.J. / Blass, S. / Berger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wbz.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbz.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbz ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbz | HTTPS FTP |
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-Related structure data
Related structure data | 2vhkC 2vhrC 2vi1C 2vi2C 2vi3C 2vi4C 2vu6C 2vu7C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22155.980 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-206 / Source method: isolated from a natural source / Details: FROM ARIL COVERING SEEDS / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 7.3 Details: PROTEIN AT 47 MG/ML IN 10MM SODIUM PHOSPHATE (PH=7.3) AND 5% (V/V) GLYCEROL; CRYSTALS GROWN AT 4 C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8209 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 24, 2007 / Details: TORROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8209 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→23 Å / Num. obs: 35012 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→21.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.181 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→21.43 Å
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Refine LS restraints |
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