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Yorodumi- PDB-7yxt: Crystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yxt | ||||||
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Title | Crystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) with different conformations for G261-G265 fragment | ||||||
Components | Indoleamine 2,3-dioxygenase 1 | ||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / Tryptophan metabolism | ||||||
Function / homology | Function and homology information indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / positive regulation of T cell apoptotic process / negative regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / T cell proliferation / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Mirgaux, M. / Wouters, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) with different conformations for G261-G265 fragment Authors: Mirgaux, M. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yxt.cif.gz | 398.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yxt.ent.gz | 262.7 KB | Display | PDB format |
PDBx/mmJSON format | 7yxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/7yxt ftp://data.pdbj.org/pub/pdb/validation_reports/yx/7yxt | HTTPS FTP |
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-Related structure data
Related structure data | 7ngeS S: Starting model for refinement |
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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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 45300.898 Da / Num. of mol.: 4 / Mutation: K116A, K117A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pet-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-OXY / | #5: 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: 3 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Well: 0.1M KH2PO4/K2HPO4 buffer at pH 6.2 supplemented with 17% of PEG 3350 solution Protein: 5 mM HEPES/NaOH pH 7.6, 200 mM NaCl, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2021 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→49.07 Å / Num. obs: 73894 / % possible obs: 99.71 % / Redundancy: 13.3 % / Biso Wilson estimate: 48.89 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1683 / Rpim(I) all: 0.04815 / Rrim(I) all: 0.1751 / Net I/σ(I): 11.01 |
Reflection shell | Resolution: 2.485→2.574 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 7203 / CC1/2: 0.802 / CC star: 0.943 / Rpim(I) all: 0.4084 / % possible all: 98.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NGE Resolution: 2.48→49.07 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3811 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→49.07 Å
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Refine LS restraints |
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LS refinement shell |
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