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Yorodumi- PDB-2vi4: Atomic resolution (1.10 A) structure of purified thaumatin I grow... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vi4 | ||||||
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Title | Atomic resolution (1.10 A) structure of purified thaumatin I grown in sodium DL-tartrate at 6 C. | ||||||
Components | THAUMATIN-1 | ||||||
Keywords | PLANT PROTEIN / KINETICS OF CRYSTALLIZATION / CHIRALITY / TEMPERATURE / MICROBATCH / SWEET PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THAUMATOCOCCUS DANIELLII (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 | 2vi4.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vi4.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vi4 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vi4 | HTTPS FTP |
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-Related structure data
Related structure data | 2vhkC 2vhrC 2vi1C 2vi2C 2vi3C 2vu6C 2vu7C 2wbzC 1kwn C: citing same article (ref.) S: Starting model for refinement |
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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: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM ARIL. / Source: (natural) THAUMATOCOCCUS DANIELLII (katemfe) / References: UniProt: P02883 | ||
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#2: Chemical | ChemComp-TLA / | ||
#3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE |
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Crystal grow | Temperature: 279 K / Method: microbatch / pH: 7.1 Details: MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM DL-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 6 C |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.1→20 Å / Num. obs: 104165 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.2 | ||||||||||||||||||
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KWN 1kwn Resolution: 1.1→19.75 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.602 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→19.75 Å
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Refine LS restraints |
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