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Yorodumi- PDB-5x6r: Crystal structure of Saccharomyces cerevisiae KMO in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x6r | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae KMO in complex with Ro 61-8048 | ||||||
Components | Kynurenine 3-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase | ||||||
Function / homology | Function and homology information Tryptophan catabolism / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic process ...Tryptophan catabolism / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.911 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 | 5x6r.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6r.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 5x6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6r ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6r | HTTPS FTP |
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-Related structure data
Related structure data | 5x68C 5x6pC 5x6qC 4j33S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 47913.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: BNA4, YBL098W, YBL0828 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P38169, kynurenine 3-monooxygenase #2: Chemical | #3: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, pH 4.6, 0.1 M NaCl, and 12% isopropanol |
-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: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Dec 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→30.797 Å / Num. obs: 72243 / % possible obs: 99.03 % / Redundancy: 3.6 % / Net I/σ(I): 27.19 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.16 / Num. unique obs: 3550 / CC1/2: 0.899 / Rpim(I) all: 0.24 / Rrim(I) all: 0.438 / Rsym value: 0.364 / Χ2: 1.674 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J33 Resolution: 1.911→30.797 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.911→30.797 Å
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Refine LS restraints |
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LS refinement shell |
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