+Open data
-Basic information
Entry | Database: PDB / ID: 8uiq | ||||||
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Title | H47Q NicC with 2-mercaptopyridine ligand | ||||||
Components | 6-hydroxynicotinate 3-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / ligand bound | ||||||
Function / homology | Function and homology information 6-hydroxynicotinate 3-monooxygenase / 6-hydroxynicotinate 3-monooxygenase activity / : / monooxygenase activity / FAD binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida KT2440 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Hicks, K.A. / Perry, K. / Turlington, Z.R. / Vaz Ferreira de Macedo, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2024 Title: Ligand bound structure of a 6-hydroxynicotinic acid 3-monooxygenase provides mechanistic insights. Authors: Turlington, Z.R. / Vaz Ferreira de Macedo, S. / Perry, K. / Belsky, S.L. / Faust, J.A. / Snider, M.J. / Hicks, K.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uiq.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uiq.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 8uiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/8uiq ftp://data.pdbj.org/pub/pdb/validation_reports/ui/8uiq | HTTPS FTP |
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-Related structure data
Related structure data | 8uivC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45420.066 Da / Num. of mol.: 1 / Mutation: H47Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: nicC / Production host: Escherichia coli (E. coli) / References: UniProt: Q88FY2 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-PYS / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes, pH 7.5, 15-25% polyethylene glycol (PEG) 3350, and 0.2 M magnesium chloride hexahydrate |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 8UIQ / CC1/2: 0.997
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Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→59.36 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 35.6149 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→59.36 Å
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Refine LS restraints |
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LS refinement shell |
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