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Yorodumi- PDB-8vg5: Crystal Structure of V113N Variant of D-Dopachrome Tautomerase (D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vg5 | ||||||
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Title | Crystal Structure of V113N Variant of D-Dopachrome Tautomerase (D-DT) Bound with 4CPPC | ||||||
Components | D-dopachrome decarboxylase | ||||||
Keywords | ISOMERASE / Truncation / Enzyme / Cytokine | ||||||
Function / homology | Function and homology information D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / melanin biosynthetic process / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade ...D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / melanin biosynthetic process / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade / extracellular space / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Parkins, A. / Pilien, A. / Thompson, M.C. / Pantouris, G. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vg5.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vg5.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 8vg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/8vg5 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/8vg5 | HTTPS FTP |
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-Related structure data
Related structure data | 8vdyC 8vfkC 8vflC 8vfnC 8vfoC 8vfwC 8vg7C 8vg8C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12608.498 Da / Num. of mol.: 4 / Mutation: V113N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDT / Production host: Escherichia coli (E. coli) / References: UniProt: P30046, D-dopachrome decarboxylase #2: Chemical | ChemComp-7L9 / | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 26-32% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate PH range: 5.2-6.8 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
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: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→55.6 Å / Num. obs: 73626 / % possible obs: 99.1 % / Redundancy: 17 % / CC1/2: 0.992 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.056 / Rrim(I) all: 0.239 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.5→1.53 Å / % possible obs: 95.2 % / Redundancy: 9.1 % / Rmerge(I) obs: 1.974 / Num. measured all: 31856 / Num. unique obs: 3502 / CC1/2: 0.481 / Rpim(I) all: 0.679 / Rrim(I) all: 2.093 / Net I/σ(I) obs: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→55.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.384 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→55.6 Å
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