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- PDB-5aew: Crystal structure of II9 variant of Biphenyl dioxygenase from Bur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aew | ||||||
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Title | Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl | ||||||
![]() | (BIPHENYL DIOXYGENASE SUBUNIT ...) x 2 | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dhindwal, S. / Gomez-Gil, L. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P. | ||||||
![]() | ![]() Title: Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase. Authors: Dhindwal, S. / Gomez-Gil, L. / Neau, D.B. / Pham, T.T.M. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.8 MB | Display | ![]() |
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PDB format | ![]() | 2.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5aeuC ![]() 2xr8S ![]() 5aev C: citing same article ( 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
-BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX
#1: Protein | Mass: 51471.262 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Variant: II9 / Plasmid: PET14B / Production host: ![]() ![]() ![]() ![]() #2: Protein | Mass: 22113.846 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Variant: II9 / Plasmid: PET14B / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 4050 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/BNL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/BNL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FES / ![]() #4: Chemical | ChemComp-FE2 / #5: Chemical | ChemComp-BNL / ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | MUTATION AT RESIDUE T335G, F336I, N338T, I341T |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % / Description: NONE |
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Crystal grow![]() | pH: 6 Details: PEG8000, 50MM MES PH 6.0, GLYCEROL 6% AND 50MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.87→129.1 Å / Num. obs: 634861 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.88→23.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2XR8 Resolution: 1.88→23.34 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.271 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.163 / 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: 41.014 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→23.34 Å
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Refine LS restraints |
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