+Open data
-Basic information
Entry | Database: PDB / ID: 2d8o | ||||||
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Title | Structure of VIL-thaumatin | ||||||
Components | Thaumatin I | ||||||
Keywords | UNKNOWN FUNCTION / iodo-tyrosine / VAPORIZING IODINE LABELING(VIL) | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.38 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 | 2d8o.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d8o.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d8o_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 2d8o_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 2d8o_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 2d8o_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/2d8o ftp://data.pdbj.org/pub/pdb/validation_reports/d8/2d8o | HTTPS FTP |
-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: 22730.646 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 | #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: 2.73 Å3/Da / Density % sol: 54.88 % |
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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 FR-E / Wavelength: 2.2908 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 20, 2004 / Details: confocal Cr mirror optics |
Radiation | Monochromator: confocal Cr mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.2908 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→53.45 Å / Num. all: 10679 / Num. obs: 9725 / % possible obs: 91.07 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.38→2.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.146 / % possible all: 32.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.38→40.41 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1281589.91 / 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: 21.91 Å2 / ksol: 0.38289 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→40.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Xplor file |
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