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- PDB-6foy: The crystal structure of P.fluorescens Kynurenine 3-monooxygenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6foy | |||||||||||||||
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Title | The crystal structure of P.fluorescens Kynurenine 3-monooxygenase (KMO) in complex with competitive inhibitor No. 9 | |||||||||||||||
![]() | Kynurenine 3-monooxygenase | |||||||||||||||
![]() | OXIDOREDUCTASE / Inhibitor | |||||||||||||||
Function / homology | ![]() 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 | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Levy, C.W. / Leys, D. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A brain-permeable inhibitor of the neurodegenerative disease target kynurenine 3-monooxygenase prevents accumulation of neurotoxic metabolites. Authors: Zhang, S. / Sakuma, M. / Deora, G.S. / Levy, C.W. / Klausing, A. / Breda, C. / Read, K.D. / Edlin, C.D. / Ross, B.P. / Wright Muelas, M. / Day, P.J. / O'Hagan, S. / Kell, D.B. / Schwarcz, R. ...Authors: Zhang, S. / Sakuma, M. / Deora, G.S. / Levy, C.W. / Klausing, A. / Breda, C. / Read, K.D. / Edlin, C.D. / Ross, B.P. / Wright Muelas, M. / Day, P.J. / O'Hagan, S. / Kell, D.B. / Schwarcz, R. / Leys, D. / Heyes, D.J. / Giorgini, F. / Scrutton, N.S. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 629.9 KB | Display | ![]() |
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PDB format | ![]() | 447.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50608.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 785 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/E0T.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/E0T.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH6.5, 18 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→67.78 Å / Num. obs: 115076 / % possible obs: 98.23 % / Redundancy: 3 % / Biso Wilson estimate: 14.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05683 / Rpim(I) all: 0.03797 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 1.65→1.709 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.6193 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 10780 / CC1/2: 0.526 / Rpim(I) all: 0.5095 / % possible all: 89.92 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: Inhouse Resolution: 1.65→67.78 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9161
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→67.78 Å
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Refine LS restraints |
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LS refinement shell |
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