+Open data
-Basic information
Entry | Database: PDB / ID: 2d8p | ||||||
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Title | Structure of HYPER-VIL-thaumatin | ||||||
Components | Thaumatin I | ||||||
Keywords | UNKNOWN FUNCTION / iodo-tyrosine / HYDROGEN PEROXIDE VAPORIZING IODINE LABELING(HYPER-VIL) | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.3 Å | ||||||
Authors | Miyatake, H. / Hasegawa, T. / Yamano, A. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL) Authors: Miyatake, H. / Hasegawa, T. / Yamano, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d8p.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d8p.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/2d8p ftp://data.pdbj.org/pub/pdb/validation_reports/d8/2d8p | HTTPS FTP |
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-Related 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: 23360.133 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-IOD / #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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8M K/Na tartrate, 0.1M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54182 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 1, 2004 / Details: Osmic Cu CMF |
Radiation | Monochromator: Osmic Cu CMF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→53.916 Å / Num. all: 21518 / Num. obs: 21518 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.8 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→31.7 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 271975.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.6777 Å2 / ksol: 0.392464 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→31.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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