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Yorodumi- PDB-8oxn: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oxn | ||||||
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Title | CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXYC CONDITIONS | ||||||
Components | 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA HYDROLASE / DIOXYGENASE / COFACTOR-DEVOID | ||||||
Function / homology | Function and homology information 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / : Similarity search - Function | ||||||
Biological species | Paenarthrobacter nitroguajacolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bui, S. / Steiner, R.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold. Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oxn.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oxn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8oxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oxn_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8oxn_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8oxn_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 8oxn_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/8oxn ftp://data.pdbj.org/pub/pdb/validation_reports/ox/8oxn | HTTPS FTP |
-Related structure data
Related structure data | 7ojmC 7okzC 8a97C 8oroC 8oxtC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 275 / Label seq-ID: 15 - 287
NCS ensembles :
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-Components
#1: Protein | Mass: 33273.391 Da / Num. of mol.: 4 / Mutation: C69S, S101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria) Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Production host: Escherichia coli (E. coli) References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase #2: Chemical | ChemComp-VFH / #3: Chemical | #4: Chemical | ChemComp-SRT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→46.56 Å / Num. obs: 86750 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Net I/σ(I): 12.7 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6256 / Rpim(I) all: 0.375 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.797 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.028 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.936 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.56 Å
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Refine LS restraints |
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