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Yorodumi- PDB-8x38: Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8x38 | ||||||
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Title | Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium | ||||||
Components | Decarboxylative Vanillate 1-Hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / flavoprotein / flavin-dependent monooxygenase / flavoprotein monooxygenases | ||||||
Function / homology | ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Phanerochaete chrysosporium RP-78 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Suzuki, H. / Mori, R. / Ishida, T. / Igarashi, K. / Shimizu, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium Authors: Mori, R. / Suzuki, H. / Ishida, T. / Igarashi, K. / Kato, M. / Shimizu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x38.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x38.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 8x38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x38_validation.pdf.gz | 746.4 KB | Display | wwPDB validaton report |
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Full document | 8x38_full_validation.pdf.gz | 748.2 KB | Display | |
Data in XML | 8x38_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 8x38_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/8x38 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/8x38 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54814.238 Da / Num. of mol.: 1 / Mutation: D169A L184V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium RP-78 (fungus) Strain: RP78 / Gene: fgenesh1_kg.3_#_10694_#_transcript/44524 / Plasmid: pQE60 Details (production host): Bacterial vector for expressing C-terminally 6xHis-tagged proteins, with an NcoI site at the start codon Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: salicylate 1-monooxygenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-ACT / |
#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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate, 18% (w/v) Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.56 Å / Num. obs: 53038 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.015 / Rrim(I) all: 0.056 / Χ2: 0.99 / Net I/σ(I): 30.3 / Num. measured all: 696271 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.872 / Num. measured all: 37527 / Num. unique obs: 2769 / CC1/2: 0.905 / Rpim(I) all: 0.244 / Rrim(I) all: 0.906 / Χ2: 0.95 / Net I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.363 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.898 Å2
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Refinement step | Cycle: 1 / Resolution: 2→46.77 Å
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Refine LS restraints |
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