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Yorodumi- PDB-6e43: Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+43 | ||||||
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Title | Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) in complex with a BMS-978587 analog | ||||||
Components | Indoleamine 2,3-dioxygenase 1 | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / IDO1 / BMS-978587 analog / inhibitor complex / oxidoreductase-oxidoreductase inhibitor complex | ||||||
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 / negative regulation of T cell apoptotic process / positive 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.705 Å | ||||||
Authors | Luo, S. / Tong, L. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form. Authors: Luo, S. / Xu, K. / Xiang, S. / Chen, J. / Chen, C. / Guo, C. / Tong, Y. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e43.cif.gz | 331.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e43.ent.gz | 268.6 KB | Display | PDB format |
PDBx/mmJSON format | 6e43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e43_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6e43_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6e43_validation.xml.gz | 67.8 KB | Display | |
Data in CIF | 6e43_validation.cif.gz | 98.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/6e43 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/6e43 | HTTPS FTP |
-Related structure data
Related structure data | 6e40C 6e41C 6e42C 6e44C 6e45C 6e46C 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
#1: Protein | Mass: 45300.898 Da / Num. of mol.: 4 / Fragment: residue 15-403 / 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 (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase #2: Chemical | ChemComp-HQM / ( #3: Chemical | ChemComp-BEZ / #4: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.2 / Details: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.705→47.642 Å / Num. obs: 201224 / % possible obs: 99.2 % / Redundancy: 4.435 % / Biso Wilson estimate: 28.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.071 / Χ2: 1.128 / Net I/σ(I): 11.52 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Resolution: 1.705→47.642 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.17 Å2 / Biso mean: 33.019 Å2 / Biso min: 15.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.705→47.642 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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