[English] 日本語
Yorodumi- PDB-5nah: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nah | ||||||
---|---|---|---|---|---|---|---|
Title | Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with 3-{5-chloro-6-[(1R)-1-(6-methylpyridazin-3-yl)ethoxy]-1,2-benzoxazol-3-yl}propanoic acid | ||||||
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: 1.75 Å | ||||||
Authors | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5nah.cif.gz | 380 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5nah.ent.gz | 318.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5nah ftp://data.pdbj.org/pub/pdb/validation_reports/na/5nah | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50787.516 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% glycerol, 14.4% PEG 8000, 0.08 M sodium cacodylate pH 6.5, 0.16 M calcium acetate or 20% glycerol, 16% PEG 8000, 0.08M sodium cacodylate pH 6.5, 0.16M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49 Å / Num. obs: 95918 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9341 / CC1/2: 0.611 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→44.05 Å / Cor.coef. Fo:Fc: 0.9621 / Cor.coef. Fo:Fc free: 0.9518 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.103
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.91 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.195 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→44.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|