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Yorodumi- PDB-6o8a: Thaumatin native-SAD structure determined at 5 keV from microcrystals -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o8a | ||||||
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Title | Thaumatin native-SAD structure determined at 5 keV from microcrystals | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / MICROCRYSTAL / MICRODIFFRACTION / NATIVE-SAD / LOW ENERGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Guo, G. / Zhu, P. / Fuchs, M.R. / Shi, W. / Andi, B. / Gao, Y. / Hendrickson, W.A. / McSweeney, S. / Liu, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: Iucrj / Year: 2019 Title: Synchrotron microcrystal native-SAD phasing at a low energy. Authors: Guo, G. / Zhu, P. / Fuchs, M.R. / Shi, W. / Andi, B. / Gao, Y. / Hendrickson, W.A. / McSweeney, S. / Liu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o8a.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o8a.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 6o8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/6o8a ftp://data.pdbj.org/pub/pdb/validation_reports/o8/6o8a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Thaumatococcus daniellii (katemfe) / 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: 2.82 Å3/Da / Density % sol: 56.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.7 M SODIUM TARTRATE, 100 MM ADA, PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 2.479 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.479 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 8435 / % possible obs: 100 % / Redundancy: 323 % / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.6→2.7 Å / Num. unique obs: 588 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→37.85 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 21.07
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→37.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.7195 Å / Origin y: 16.5942 Å / Origin z: -4.9837 Å
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Refinement TLS group | Selection details: chain A and (resseq 1:207) |