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Yorodumi- PDB-7nge: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nge | ||||||
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Title | Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed 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: 2.3 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 | 7nge.cif.gz | 405.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nge.ent.gz | 269.8 KB | Display | PDB format |
PDBx/mmJSON format | 7nge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/7nge ftp://data.pdbj.org/pub/pdb/validation_reports/ng/7nge | HTTPS FTP |
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-Related structure data
Related structure data | 7p0nC 7p0rC 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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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 on special symmetry positions |
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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 Details: Monomer A / Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase |
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-Non-polymers , 8 types, 716 molecules
#2: Chemical | ChemComp-TRP / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-NA / | #7: Chemical | #8: Chemical | ChemComp-CL / | #9: 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: 3.04 Å3/Da / Density % sol: 59.59 % / Description: Red rectangular crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15.4% PEG 3350 0.1M Phosphate buffer pH 6.0 Protein : 5mM HEPES pH 7.4, 200mM NaCl, 5mM 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: 0.979 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: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.87 Å / Num. obs: 91724 / % possible obs: 99.56 % / Redundancy: 12.2 % / Biso Wilson estimate: 46.98 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.2072 / Rpim(I) all: 0.06342 / Rrim(I) all: 0.217 / Net I/σ(I): 10.43 |
Reflection shell | Resolution: 2.301→2.384 Å / Redundancy: 11.6 % / Rmerge(I) obs: 2.655 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 8917 / CC1/2: 0.541 / CC star: 0.838 / Rpim(I) all: 0.8097 / Rrim(I) all: 2.778 / % possible all: 97.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7A62 Resolution: 2.3→46.87 Å / SU ML: 0.2926 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5976 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: 54.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.87 Å
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Refine LS restraints |
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LS refinement shell |
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