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Yorodumi- PDB-4u74: Crystal structure of 4-phenylimidazole bound form of human indole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u74 | |||||||||||||||
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Title | Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (G262A mutant) | |||||||||||||||
Components | Indoleamine 2,3-dioxygenase 1 | |||||||||||||||
Keywords | OXIDOREDUCTASE / metal-binding / all alpha | |||||||||||||||
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: 2.31 Å | |||||||||||||||
Authors | Sugimoto, H. / Horitani, M. / Kometani, E. / Shiro, Y. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: to be published Title: Conformation and Mobility of Active Site Loop is Critical for Substrate Binding and Inhibition in Human Indoleamine 2,3-Dioxygenase Authors: Horitani, M. / Kometani, E. / Vottero, E. / Otsuki, T. / Shiro, Y. / Sugimoto, H. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006 Title: Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase. Authors: Sugimoto, H. / Oda, S. / Otsuki, T. / Hino, T. / Yoshida, T. / Shiro, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u74.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u74.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 4u74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/4u74 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/4u74 | HTTPS FTP |
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-Related structure data
Related structure data | 4u72C 2d0tS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 12 - 403 / Label seq-ID: 15 - 406
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-Components
#1: Protein | Mass: 45680.508 Da / Num. of mol.: 2 / Mutation: G262A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: P14902, indoleamine 2,3-dioxygenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NHE / #5: 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: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 12 % (W/V) PEG 8000, 0.2 M ammonium acetate, 1 mM 4-phenylimidazole, 0.1 M CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors |
Diffraction measurement | Details: 0.60 degrees, 4.0 sec, detector distance 200.00 mm / Method: \w scans |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.079 / Number: 368971 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 50474 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 26.59 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.691 / Rsym value: 0.685 / % possible all: 100 |
Cell measurement | Reflection used: 368971 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D0T Resolution: 2.31→19.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1866 / WRfactor Rwork: 0.1468 / FOM work R set: 0.8491 / SU B: 5.55 / SU ML: 0.133 / SU R Cruickshank DPI: 0.2239 / SU Rfree: 0.1927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.84 Å2 / Biso mean: 33.992 Å2 / Biso min: 14.83 Å2
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Refinement step | Cycle: final / Resolution: 2.31→19.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 467 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.307→2.366 Å / Total num. of bins used: 20
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