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- PDB-5aeu: 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: 5aeu | ||||||
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Title | Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 | ||||||
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![]() | OXIDOREDUCTASE / BPHAE-II9 / BIPHENYL / POLYCHLORINATED BIPHENYLS | ||||||
Function / homology | ![]() biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / 3-phenylpropionate catabolic process / : / 2 iron, 2 sulfur cluster binding / iron ion binding 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: Kumar, P. / Dhindwal, S. / Neau, D. / Gomez-Gil, L. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 496 KB | Display | ![]() |
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PDB format | ![]() | 408.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.5 KB | Display | ![]() |
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Full document | ![]() | 548.7 KB | Display | |
Data in XML | ![]() | 87.2 KB | Display | |
Data in CIF | ![]() | 119.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5aewC ![]() 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 51471.262 Da / Num. of mol.: 4 / 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.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Variant: II9 / Plasmid: PET14B / Production host: ![]() ![]() #3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FE2 / #5: Water | ChemComp-HOH / | 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: 2.48 Å3/Da / Density % sol: 50.42 % / Description: NONE |
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Crystal grow | pH: 6 Details: PEG8000, 50MM MES PH 6.0, 6% GLYCEROL AND 50 MM 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→129.1 Å / Num. obs: 97519 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.49→2.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XR8 Resolution: 2.49→38.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.791 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.632 / ESU R Free: 0.301 / 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: 59.624 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→38.56 Å
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Refine LS restraints |
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