+Open data
-Basic information
Entry | Database: PDB / ID: 8hvf | ||||||||||||
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Title | Crystal structure of Thaumatin (100 ms) | ||||||||||||
Components | Thaumatin I | ||||||||||||
Keywords | PLANT PROTEIN / thaumatin / radiation damage | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | ||||||||||||
Authors | Nam, K.H. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: To Be Published Title: Crystal structure of Thaumatin (100 ms) Authors: Nam, K.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hvf.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hvf.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/8hvf ftp://data.pdbj.org/pub/pdb/validation_reports/hv/8hvf | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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 natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 | ||||
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#2: Chemical | ChemComp-TLA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, hanging drop / Details: tartrate acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→45.91 Å / Num. obs: 2350491 / % possible obs: 99.89 % / Redundancy: 24.3 % / CC1/2: 0.999 / Net I/σ(I): 11.37 |
Reflection shell | Resolution: 1.13→1.17 Å / Num. unique obs: 9513 / CC1/2: 0.647 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→45.91 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.17 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→45.91 Å
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Refine LS restraints |
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LS refinement shell |
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