+Open data
-Basic information
Entry | Database: PDB / ID: 5x68 | ||||||
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Title | Crystal Structure of Human KMO | ||||||
Components | Kynurenine 3-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase / flavin reduction | ||||||
Function / homology | Function and homology information L-kynurenine metabolic process / positive regulation of glutamate secretion, neurotransmission / : / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / kynurenic acid biosynthetic process / anthranilate metabolic process / : ...L-kynurenine metabolic process / positive regulation of glutamate secretion, neurotransmission / : / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / kynurenic acid biosynthetic process / anthranilate metabolic process / : / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / NAD metabolic process / cellular response to interleukin-1 / response to salt stress / FAD binding / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / membrane => GO:0016020 / mitochondrion / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kim, H.T. / Hwang, K.Y. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2018 Title: Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase Authors: Kim, H.T. / Na, B.K. / Chung, J. / Kim, S. / Kwon, S.K. / Cha, H. / Son, J. / Cho, J.M. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x68.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x68.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 5x68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x68 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x68 | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 44285.121 Da / Num. of mol.: 2 / Fragment: UNP residues 1-374 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KMO / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O15229, kynurenine 3-monooxygenase #2: Chemical | #3: 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: 3.17 Å3/Da / Density % sol: 61.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris (pH 8.5), 13% polyethylene glycol 4000, and 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: AREA DETECTOR / Date: Dec 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→88.37 Å / Num. obs: 55790 / % possible obs: 96.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.063 / Net I/σ(I): 25.6 |
Reflection shell | Redundancy: 2.4 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.315 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→88.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.433 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→88.37 Å
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Refine LS restraints |
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