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- PDB-3u52: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u52 | ||||||
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Title | X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1 | ||||||
![]() | (Phenol hydroxylase component ...) x 3 | ||||||
![]() | OXIDOREDUCTASE / 4-Helix Bundle / Hydroxylase / Dioxygen / Hydrocarbons | ||||||
Function / homology | ![]() phenol 2-monooxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McCormick, M.S. / Lippard, S.J. | ||||||
![]() | ![]() Title: Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1. Authors: McCormick, M.S. / Lippard, S.J. #1: Journal: Biochemistry / Year: 2011 Title: Correction to Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1. Authors: McCormick, M.S. / Lippard, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 400.3 KB | Display | ![]() |
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PDB format | ![]() | 323.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 524.4 KB | Display | ![]() |
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Full document | ![]() | 568.2 KB | Display | |
Data in XML | ![]() | 75.4 KB | Display | |
Data in CIF | ![]() | 103.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2innS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Phenol hydroxylase component ... , 3 types, 6 molecules ABCDEF
#1: Protein | Mass: 60217.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Alpha Subunit / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 38458.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Beta Subunit / Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13248.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Gamma Subunit / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 632 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-FE / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-XE / #9: Chemical | ChemComp-MPO / | #10: Chemical | ChemComp-EPE / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Tris (pH 7.0), 150 mM Na2MoO4, 5% glycerol (v/v), 19% PEG 8000 (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 24, 2006 / Details: Mirrors |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38 Å / Num. all: 149674 / Num. obs: 138448 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 |
Reflection shell | Resolution: 1.95→2 Å / % possible all: 82.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 2INN Resolution: 1.95→38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.95 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.577 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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