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Yorodumi- PDB-8ena: Thaumatin native-SAD structure determined at 5 keV with a helium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ena | ||||||
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Title | Thaumatin native-SAD structure determined at 5 keV with a helium environmet | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / anomalous diffration / native SAD / low energy / helium path | ||||||
Function / homology | Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / cytoplasmic vesicle / Thaumatin I Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Karasawa, A. / Andi, B. / Ruchs, M.R. / Shi, W. / McSweeney, S. / Hendrickson, W.A. / Liu, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: Iucrj / Year: 2022 Title: Multi-crystal native-SAD phasing at 5 keV with a helium environment. Authors: Karasawa, A. / Andi, B. / Fuchs, M.R. / Shi, W. / McSweeney, S. / Hendrickson, W.A. / Liu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ena.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ena.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ena.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/8ena ftp://data.pdbj.org/pub/pdb/validation_reports/en/8ena | HTTPS FTP |
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-Related structure data
Related structure data | 8en9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 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: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.7 M sodium tartrate, 100 mM ADA, pH 6.5 |
-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: Jun 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.479 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.34 Å / Num. obs: 16225 / % possible obs: 97.1 % / Redundancy: 183.6 % / Biso Wilson estimate: 27.96 Å2 / CC1/2: 0.979 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.5→2.53 Å / Num. unique obs: 372 / CC1/2: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→39.34 Å / SU ML: 0.3944 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3247 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: 25.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.34 Å
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Refine LS restraints |
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LS refinement shell |
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