[English] 日本語
Yorodumi- PDB-8vfo: Crystal Structure of L117G Variant of D-Dopachrome Tautomerase (D-DT) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vfo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of L117G Variant of D-Dopachrome Tautomerase (D-DT) | ||||||
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: 1.35 Å | ||||||
Authors | Parkins, A. / Pilien, A. / Thompson, M.C. / Pantouris, G. | ||||||
Funding support | 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vfo.cif.gz | 40 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vfo.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 8vfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/8vfo ftp://data.pdbj.org/pub/pdb/validation_reports/vf/8vfo | HTTPS FTP |
---|
-Related structure data
Related structure data | 8vdyC 8vfkC 8vflC 8vfnC 8vfwC 8vg5C 8vg7C 8vg8C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12537.421 Da / Num. of mol.: 1 / Mutation: L117G 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-CIT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20-28% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate PH range: 5.8 - 6.2 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 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: 1.35→40.29 Å / Num. obs: 21271 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.025 / Rrim(I) all: 0.056 / Net I/σ(I): 20.4 / Num. measured all: 96387 |
Reflection shell | Resolution: 1.35→1.37 Å / % possible obs: 94.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.252 / Num. measured all: 2853 / Num. unique obs: 1008 / CC1/2: 0.902 / Rpim(I) all: 0.171 / Rrim(I) all: 0.306 / Net I/σ(I) obs: 3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→40.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 9.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|