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- PDB-8x38: Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8x38 | ||||||
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Title | Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium | ||||||
![]() | Decarboxylative Vanillate 1-Hydroxylase | ||||||
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Function / homology | ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, H. / Mori, R. / Ishida, T. / Igarashi, K. / Shimizu, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() 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: ![]() ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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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