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- PDB-4bal: Thaumatin from Thaumatococcus daniellii structure in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bal | ||||||
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Title | Thaumatin from Thaumatococcus daniellii structure in complex with the europium tris-hydroxymethyltriazoledipicolinate complex at 1.30 A resolution. | ||||||
![]() | THAUMATIN-1 | ||||||
![]() | PLANT PROTEIN / CLICK-CHEMISTRY / ANOMALOUS SCATTERING / DE NOVO PHASING / EXPERIMENTAL PHASING / DIPICOLINATE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Talon, R. / Kahn, R. / Gautier, A. / Nauton, L. / Girard, E. | ||||||
![]() | ![]() Title: Clicked Europium Dipicolinate Complexes for Protein X-Ray Structure Determination. Authors: Talon, R. / Nauton, L. / Canet, J.-L. / Kahn, R. / Girard, E. / Gautier, A. #1: ![]() Title: Protein Crystallography Through Supramolecular Interactions between a Lanthanide Complex and Arginine. Authors: Pompidor, G. / D'Aleo, A. / Vicat, J. / Toupet, L. / Giraud, N. / Kahn, R. / Maury, O. #2: ![]() Title: A Dipicolinate Lanthanide Complex for Solving Protein Structures Using Anomalous Diffraction. Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R. #3: ![]() Title: Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme. Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.9 KB | Display | ![]() |
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PDB format | ![]() | 87.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4badC ![]() 4bafC ![]() 4bapC ![]() 4barSC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH POWDER, CATALOG REFERENCE T7638 / Source: (natural) ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-EU3 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 0.1 M BIS-TRIS PROPANE PH 6.5, 0.3-0.9 SODIUM POTASSIUM TARTRATE, 0.0006 M PROTEIN, 0.010 M LANTHANIDE COMPLEX, 293 K, 5 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2010 / Details: MIRRORS |
Radiation | Monochromator: EITHER 111 OR 311 SILICON SINGLE CRISTALS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→45.9 Å / Num. obs: 64239 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BAR Resolution: 1.298→28.994 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 11.87 / Stereochemistry target values: ML Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS. LIGANDS OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCY.
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.309 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.298→28.994 Å
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Refine LS restraints |
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LS refinement shell |
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