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Yorodumi- PDB-6ybx: RT structure of Thaumatin obtained at 1.14 A resolution from crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ybx | ||||||
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Title | RT structure of Thaumatin obtained at 1.14 A resolution from crystal grown in a Mylar microchip. | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / SWEET TASTING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Gavira, J.A. / Martinez-Rodriguez, S. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Authors: Gavira, J.A. / Rodriguez-Ruiz, I. / Martinez-Rodriguez, S. / Basu, S. / Teychene, S. / McCarthy, A.A. / Mueller-Dieckman, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ybx.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ybx.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 6ybx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ybx_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 6ybx_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 6ybx_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 6ybx_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/6ybx ftp://data.pdbj.org/pub/pdb/validation_reports/yb/6ybx | HTTPS FTP |
-Related structure data
Related structure data | 6ybfC 6ybiC 6yboC 6ybrC 6yc5C 1thwS 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) / References: UniProt: P02883 |
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#2: Chemical | ChemComp-TLA / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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 % |
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Crystal grow | Temperature: 293.5 K / Method: counter-diffusion / pH: 7 / Details: 20% w/v NaK Tartrate / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 293.5 K / Ambient temp details: Room Temperature / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017 Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→46.34 Å / Num. obs: 89815 / % possible obs: 92.35 % / Redundancy: 31.69 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.14→1.18 Å / Num. unique obs: 5094 / CC1/2: 0.791 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1THW Resolution: 1.14→46.34 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4692 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 22.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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