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- PDB-2yfj: Crystal structure of Biphenyl dioxygenase variant RR41 with diben... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yfj | ||||||
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Title | Crystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran | ||||||
![]() | (BIPHENYL DIOXYGENASE SUBUNIT ...) x 2 | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Sylvestre, M. / Bolin, J.T. | ||||||
![]() | ![]() Title: Retuning Rieske-Type Oxygenases to Expand Substrate Range. Authors: Mohammadi, M. / Viger, J. / Kumar, P. / Barriault, D. / Bolin, J.T. / Sylvestre, 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 | ![]() | 717.6 KB | Display | ![]() |
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PDB format | ![]() | 589 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yfiC ![]() 2xr8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 51562.398 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 22113.846 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 667 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/1IT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/1IT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FES / ![]() #4: Chemical | ChemComp-FE2 / #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 335 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 336 TO MET ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow![]() | pH: 6 / Details: PEG 5000 MME AND PIPES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Jul 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→100 Å / Num. obs: 210175 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.02 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 80 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2XR8 Resolution: 2.15→138.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.747 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.21 / 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: 42.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→138.68 Å
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Refine LS restraints |
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