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- PDB-8vdy: Crystal Structure of Delta 114-117 D-Dopachrome Tautomerase (D-DT) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vdy | ||||||
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Title | Crystal Structure of Delta 114-117 D-Dopachrome Tautomerase (D-DT) | ||||||
![]() | D-dopachrome decarboxylase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Parkins, A. / Pilien, A. / Wolff, A. / Thompson, M.C. / Pantouris, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes. Authors: Parkins, A. / Pilien, A.V.R. / Wolff, A.M. / Argueta, C. / Vargas, J. / Sadeghi, S. / Franz, A.H. / Thompson, M.C. / Pantouris, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.5 KB | Display | ![]() |
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PDB format | ![]() | 189.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8vfkC ![]() 8vflC ![]() 8vfnC ![]() 8vfoC ![]() 8vfwC ![]() 8vg5C ![]() 8vg7C ![]() 8vg8C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 12100.895 Da / Num. of mol.: 12 / Mutation: Delta 114-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.26 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 26-32% PEG 3350, 0.25-0.275M Ammonium Acetate. |
-Data collection
Diffraction | Mean temperature: 290 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.44→89.84 Å / Num. obs: 51582 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.953 / Rmerge(I) obs: 0.267 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.44→2.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 1 / Num. unique obs: 51582 / CC1/2: 0.25 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.14 Å2
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Refinement step | Cycle: 1 / Resolution: 2.44→89.84 Å
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Refine LS restraints |
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