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- PDB-8jqq: Protocatecuate hydroxylase from Xylophilus ampelinus C347T mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jqq | |||||||||
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Title | Protocatecuate hydroxylase from Xylophilus ampelinus C347T mutant | |||||||||
![]() | 4-hydroxybenzoate 3-monooxygenase (NAD(P)H) | |||||||||
![]() | OXIDOREDUCTASE / p-hydroxybenzoate hydroxylase / FAD / NADPH | |||||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fukushima, R. / Katsuki, N. / Fushinobu, S. / Takaya, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism. Authors: Katsuki, N. / Fukushima, R. / Doi, Y. / Masuo, S. / Arakawa, T. / Yamada, C. / Fushinobu, S. / Takaya, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.5 KB | Display | ![]() |
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PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 947.2 KB | Display | ![]() |
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Full document | ![]() | 952.3 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jqoC ![]() 8jqpC ![]() 1k0iS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45529.707 Da / Num. of mol.: 2 / Mutation: C347T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 8000, 0.24 M Calcium acetate, 0.1 M Imidazole |
-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: May 30, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→49.2 Å / Num. obs: 47447 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.06→2.12 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 24350 / CC1/2: 0.883 / Rpim(I) all: 0.271 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K0I Resolution: 2.06→46.38 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.9938 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→46.38 Å
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Refine LS restraints |
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LS refinement shell |
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