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Yorodumi- PDB-7qr6: Stilbene dioxygenase (NOV1) from Novosphingobium aromaticivorans:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qr6 | ||||||
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Title | Stilbene dioxygenase (NOV1) from Novosphingobium aromaticivorans: Ser283Phe mutant | ||||||
Components | Dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Iron / Dioxygenase / Biocatalysis / Carotenoid Cleavage Oxygenases / Non-heme iron proteins / Biorefinery / Lignin valorization / Thermostability | ||||||
Function / homology | 9-cis-epoxycarotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / OXYGEN MOLECULE / Dioxygenase Function and homology information | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Alvigini, L. / Mattevi, A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Rationally Guided Improvement of NOV1 Dioxygenase for the Conversion of Lignin-Derived Isoeugenol to Vanillin. Authors: De Simone, M. / Alvigini, L. / Alonso-Cotchico, L. / Brissos, V. / Caroli, J. / Lucas, M.F. / Monza, E. / Melo, E.P. / Mattevi, A. / Martins, L.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qr6.cif.gz | 287.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qr6.ent.gz | 232.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qr6_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 7qr6_full_validation.pdf.gz | 478 KB | Display | |
Data in XML | 7qr6_validation.xml.gz | 30 KB | Display | |
Data in CIF | 7qr6_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/7qr6 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qr6 | HTTPS FTP |
-Related structure data
Related structure data | 5j55S S: Starting model for refinement |
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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: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 55544.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199 Gene: Saro_0802 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) References: UniProt: Q2GA76, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Chemical | #3: Chemical | #4: 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: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: sitting drop vapour diffusion, 0.16 M MgCl2, 0.08 M Tris/HCl pH 8.5, 18% wt/vol PEG 4000, and 20% vol/vol glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999977 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999977 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 36348 / % possible obs: 91.9 % / Redundancy: 3.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.079 / Rrim(I) all: 0.146 / Rsym value: 0.092 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.9→3.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.917 / Num. unique obs: 4697 / CC1/2: 0.302 / Rpim(I) all: 0.627 / Rrim(I) all: 1.121 / Rsym value: 0.731 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J55 Resolution: 2.9→49.04 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.872 / SU B: 24.56 / SU ML: 0.437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.35 Å2 / Biso mean: 67.13 Å2 / Biso min: 34.13 Å2
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Refinement step | Cycle: final / Resolution: 2.9→49.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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