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Yorodumi- PDB-8r2u: Crystal structure of hydroquinone-2-hydroxylase from Trametes ver... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r2u | ||||||
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Title | Crystal structure of hydroquinone-2-hydroxylase from Trametes versicolor (TvMNX3) | ||||||
Components | Phenol 2-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / fungi / hydroquinone / hydroxylase | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Trametes versicolor (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Zahn, M. / Kuatsjah, E. / Salvachua, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Biochemical and structural characterization hydroquinone catabolic pathway from white-rot fungi Authors: Schwartz, A. / Kuatsjah, E. / Zahn, M. / Salvachua, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r2u.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8r2u.ent.gz | 769.5 KB | Display | PDB format |
PDBx/mmJSON format | 8r2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r2u_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8r2u_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8r2u_validation.xml.gz | 98 KB | Display | |
Data in CIF | 8r2u_validation.cif.gz | 127.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/8r2u ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r2u | HTTPS FTP |
-Related structure data
Related structure data | 8r2tC 8r2vC 8r2wC 8r2xC 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: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 5 - 606 / Label seq-ID: 5 - 606
NCS ensembles :
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-Components
#1: Protein | Mass: 68961.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes versicolor (fungus) / Gene: TRAPUB_13730 / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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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: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Structure Screen 1+2 from Molecular Dimensions condition E12 (10 % PEG 6000, 5% MPD, 0.1 M HEPES pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 31, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.408→107.884 Å / Num. obs: 78277 / % possible obs: 92.4 % / Redundancy: 5.2 % / CC1/2: 0.973 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.134 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.408→2.595 Å / Redundancy: 5 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3915 / CC1/2: 0.648 / Rpim(I) all: 0.464 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→107.884 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 23.223 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R Free: 0.32 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: 26.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→107.884 Å
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Refine LS restraints |
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