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Yorodumi- PDB-5x6q: Crystal structure of Pseudomonas fluorescens KMO in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x6q | ||||||
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Title | Crystal structure of Pseudomonas fluorescens KMO in complex with Ro 61-8048 | ||||||
Components | Kynurenine 3-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / monoxygenase | ||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 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 | 5x6q.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6q.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 5x6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6q ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6q | HTTPS FTP |
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-Related structure data
Related structure data | 5x68C 5x6pC 5x6rC 5fn0S 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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Unit cell |
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-Components
#1: Protein | Mass: 50883.648 Da / Num. of mol.: 1 / Mutation: C252S,C461S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q84HF5, kynurenine 3-monooxygenase | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.08 M sodium cacodylate (pH 6.5), 0.16 M calcium acetate, 14.4% polyethylene glycol 8000, and 20% 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: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: May 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.897→33.653 Å / Num. obs: 35769 / % possible obs: 97.64 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.047 / Rrim(I) all: 0.084 / Rsym value: 0.069 / Χ2: 2.615 / Net I/σ(I): 30.96 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1786 / CC1/2: 0.838 / Rpim(I) all: 0.241 / Rrim(I) all: 0.447 / Rsym value: 0.375 / Χ2: 1.048 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FN0 Resolution: 1.897→33.653 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.897→33.653 Å
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Refine LS restraints |
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LS refinement shell |
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