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Yorodumi- PDB-3zej: Thaumatin structure determined at room temperature by in-situ dif... -
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-Basic information
Entry | Database: PDB / ID: 3zej | ||||||
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Title | Thaumatin structure determined at room temperature by in-situ diffraction in ChipX | ||||||
Components | THAUMATIN-1 | ||||||
Keywords | PLANT PROTEIN / MICROFLUIDIC CHIP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THAUMATOCOCCUS DANIELLII (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Pinker, F. / Lorber, B. / Sauter, C. | ||||||
Citation | Journal: To be Published Title: Chipx: A Novel Microfluidic Chip for Counter- Diffusion Crystallization of Biomolecules and in Situ Crystal Analysis at Room Temperature Authors: Pinker, F. / Brun, M. / Morin, P. / Deman, A. / Chateaux, J. / Olieric, V. / Stirnimann, C. / Lorber, B. / Terrier, N. / Ferrigno, R. / Sauter, C. #1: Journal: Lab Chip / Year: 2009 Title: Microfluidic Chips for the Crystallization of Biomacromolecules by Counter-Diffusion and on-Chip Crystal X-Ray Analysis. Authors: Dhouib, K. / Khan Malek, C. / Pfleging, W. / Gauthier-Manuel, B. / Duffait, R. / Thuillier, G. / Ferrigno, R. / Jacquamet, L. / Ohana, J. / Ferrer, J. / Theobald-Dietrich, A. / Giege, R. / ...Authors: Dhouib, K. / Khan Malek, C. / Pfleging, W. / Gauthier-Manuel, B. / Duffait, R. / Thuillier, G. / Ferrigno, R. / Jacquamet, L. / Ohana, J. / Ferrer, J. / Theobald-Dietrich, A. / Giege, R. / Lorber, B. / Sauter, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zej.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zej.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3zej ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3zej | HTTPS FTP |
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-Related structure data
Related structure data | 3zekC 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 / Source: (natural) THAUMATOCOCCUS DANIELLII (katemfe) / Organ: FRUIT / References: UniProt: P02883 |
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#2: Chemical | ChemComp-TLA / |
#3: 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: 2.9 Å3/Da / Density % sol: 58.1 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 6.5 Details: THAUMATIN WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 30 MG/ML THAUMATIN SOLUTION CONTAINING 0.3% BETA-OCTYL- ...Details: THAUMATIN WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 30 MG/ML THAUMATIN SOLUTION CONTAINING 0.3% BETA-OCTYL-GLUCOSIDE (M/V) TO FACILITATE SAMPLE LOADING BY CAPILLARITY. CRYSTALLANT RESERVOIRS WERE FILLED WITH 1.5 M SODIUM TARTRATE AND 0.1 M ADA PH 6.5. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→60 Å / Num. obs: 39090 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 16.89 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.04 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KWN 1kwn Resolution: 1.55→46.368 Å / SU ML: 0.1 / σ(F): 3.04 / Phase error: 17.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→46.368 Å
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Refine LS restraints |
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LS refinement shell |
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