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Yorodumi- PDB-5nak: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nak | ||||||
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Title | Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with the enzyme substrate L-kynurenine | ||||||
Components | Kynurenine 3-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / KMO | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Taylor, M. / Mowat, C.G. / Rowland, P. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural and mechanistic basis of differentiated inhibitors of the acute pancreatitis target kynurenine-3-monooxygenase. Authors: Hutchinson, J.P. / Rowland, P. / Taylor, M.R.D. / Christodoulou, E.M. / Haslam, C. / Hobbs, C.I. / Holmes, D.S. / Homes, P. / Liddle, J. / Mole, D.J. / Uings, I. / Walker, A.L. / Webster, S. ...Authors: Hutchinson, J.P. / Rowland, P. / Taylor, M.R.D. / Christodoulou, E.M. / Haslam, C. / Hobbs, C.I. / Holmes, D.S. / Homes, P. / Liddle, J. / Mole, D.J. / Uings, I. / Walker, A.L. / Webster, S.P. / Mowat, C.G. / Chung, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nak.cif.gz | 379.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nak.ent.gz | 317.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5nak ftp://data.pdbj.org/pub/pdb/validation_reports/na/5nak | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50739.520 Da / Num. of mol.: 2 / Mutation: C252S C461S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG / Production host: Escherichia coli (E. coli) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase |
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-Non-polymers , 5 types, 1091 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-KYN / ( | #6: 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: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% glycerol, 11.0% PEG 8000, 0.08 M sodium cacodylate pH 7.0, 0.16 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→68 Å / Num. obs: 155570 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 22560 / CC1/2: 0.495 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→67.48 Å / Cor.coef. Fo:Fc: 0.9626 / Cor.coef. Fo:Fc free: 0.9562 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.072
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Displacement parameters | Biso mean: 29.45 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→67.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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