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Yorodumi- PDB-7z2l: Crystal structure of L-Kynurenine in the active site of human Ind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z2l | ||||||
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Title | Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1) | ||||||
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: 2.56 Å | ||||||
Authors | Mirgaux, M. / Wouters, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1) 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 | 7z2l.cif.gz | 406.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z2l.ent.gz | 267.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z2l ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z2l | 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
-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: pet28-a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P14902, indoleamine 2,3-dioxygenase |
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-Non-polymers , 5 types, 929 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-KYN / ( #5: Chemical | #6: 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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: Red rectangular crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Well : 0.1M Phosphate buffer, pH= 6.2, PEG 3350 = 16% Protein: 5mM Hepes, 200mM NaCl, 5mM DTT 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: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2021 / Details: channel-cut |
Radiation | Monochromator: channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→47.23 Å / Num. obs: 66614 / % possible obs: 99.18 % / Redundancy: 13.6 % / Biso Wilson estimate: 42.15 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.09638 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 2.562→2.654 Å / Mean I/σ(I) obs: 2.22 / Num. unique obs: 6308 / CC1/2: 0.855 / CC star: 0.96 / Rpim(I) all: 0.5299 / % possible all: 93.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NGE Resolution: 2.56→47.23 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4074 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: 46.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→47.23 Å
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Refine LS restraints |
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LS refinement shell |
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