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- PDB-2rdb: X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rdb | ||||||
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Title | X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant | ||||||
![]() | (Toluene, o-xylene monooxygenase oxygenase subunit; ...![]() | ||||||
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Function / homology | ![]() 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 / : / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murray, L.J. / Garcia-Serres, R. / McCormick, M.S. / Davydov, R. / Naik, S. / Hoffman, B.M. / Huynh, B.H. / Lippard, S.J. | ||||||
![]() | ![]() Title: Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase. Authors: Murray, L.J. / Garcia-Serres, R. / McCormick, M.S. / Davydov, R. / Naik, S.G. / Kim, S.H. / Hoffman, B.M. / Huynh, B.H. / 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 | ![]() | 201.8 KB | Display | ![]() |
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PDB format | ![]() | 158.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2incS 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
-Toluene, o-xylene monooxygenase oxygenase subunit; ... , 3 types, 3 molecules ABC
#1: Protein | ![]() Mass: 57859.758 Da / Num. of mol.: 1 / Mutation: I100W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 38381.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 9986.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 164 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ![]() #5: Chemical | ChemComp-P6G / | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-MPO / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 2.1-2.5 M Ammonium Sulfate, 2-4% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2006 Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→50 Å / Num. all: 75743 / Num. obs: 73939 / % possible obs: 85 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.064 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 19.4 / Rsym value: 0.541 / % possible all: 83.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2INC Resolution: 2.1→36.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.029 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.226 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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