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Yorodumi- PDB-4bar: Thaumatin from Thaumatococcus daniellii structure in complex with... -
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-Basic information
Entry | Database: PDB / ID: 4bar | |||||||||
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Title | Thaumatin from Thaumatococcus daniellii structure in complex with the europium tris-hydroxyethyltriazoledipicolinate complex at 1.20 A resolution. | |||||||||
Components | THAUMATIN-1 | |||||||||
Keywords | PLANT PROTEIN / CLICK-CHEMISTRY / DE NOVO PHASING / EXPERIMENTAL PHASING / LANTHANIDE COMPLEX / ANOMALOUS SCATTERING | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | THAUMATOCOCCUS DANIELLII (katemfe) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å | |||||||||
Authors | Talon, R. / Kahn, R. / Gautier, A. / Nauton, L. / Girard, E. | |||||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2012 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: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008 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: Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: A Dipicolinate Lanthanide Complex for Solving Protein Structures Using Anomalous Diffraction. Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bar.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bar.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/4bar ftp://data.pdbj.org/pub/pdb/validation_reports/ba/4bar | HTTPS FTP |
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-Related structure data
-Links
-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) THAUMATOCOCCUS DANIELLII (katemfe) / References: UniProt: P02883 | ||||
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#2: Chemical | #3: Chemical | ChemComp-EU3 / | #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: 2.83 Å3/Da / Density % sol: 56.5 % Description: MAD DATA AT TWO WAVELENGTHS WERE COLLECTED. THE FIRST DATA SET AT THE EUROPIUM LIII EDGE AND THE SECOND ONE AT THE SELENIUM K EDGE |
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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 M SODIUM POTASSIUM TARTRATE, 0.0006 M PROTEIN, 0.0014 M LANTHANIDE COMPLEX, 293 K, 5 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / 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: 1.2→45.83 Å / Num. obs: 78373 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 9.9 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 10 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.7 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.2→31.499 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 12.29 / Stereochemistry target values: ML Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS. LIGAND OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCIES
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.64 Å2 / ksol: 0.397 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→31.499 Å
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Refine LS restraints |
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LS refinement shell |
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