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Yorodumi- PDB-7p0r: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p0r | ||||||
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Title | Crystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) complex with the JK-loop refined in the intermediate conformation | ||||||
Components | Indoleamine 2,3-dioxygenase 1 | ||||||
Keywords | OXIDOREDUCTASE / L-TRP METABOLISM / HEMOPROTEIN / DYNAMICS LOOP | ||||||
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: 2.5 Å | ||||||
Authors | Mirgaux, M. / Wouters, J. | ||||||
Citation | Journal: Int J Tryptophan Res / Year: 2021 Title: Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site. Authors: Mirgaux, M. / Leherte, L. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p0r.cif.gz | 398.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p0r.ent.gz | 263.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0r ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0r | HTTPS FTP |
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-Related structure data
Related structure data | 7ngeC 7p0nC 7a62S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#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: pet28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase |
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-Non-polymers , 6 types, 525 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.81 Å3/Da / Density % sol: 56.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Phosphate buffer 15.4% PEG 3350 Protein buffer : 5mM Hepes, 200 mM NaCl, 5 mM DTT Cryoprotection : 20% glycerol, 20 mM sodium dithionite PH range: 6.0-6.4 / Temp details: Room Temperature |
-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: 0.98012 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 5, 2020 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98012 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.22 Å / Num. obs: 71454 / % possible obs: 99.65 % / Redundancy: 7.21 % / Biso Wilson estimate: 54.62 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 7.21 |
Reflection shell | Resolution: 2.5→2.589 Å / Mean I/σ(I) obs: 0.79 / Num. unique obs: 7008 / CC1/2: 0.59 / CC star: 0.861 / % possible all: 99.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7A62 Resolution: 2.5→49.22 Å / SU ML: 0.3843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1085 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: 61.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.22 Å
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Refine LS restraints |
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LS refinement shell |
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