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Yorodumi- PDB-5aeu: Crystal structure of II9 variant of Biphenyl dioxygenase from Bur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aeu | ||||||
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Title | Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / BPHAE-II9 / BIPHENYL / POLYCHLORINATED BIPHENYLS | ||||||
Function / homology | Function and homology information biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / aromatic compound catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | BURKHOLDERIA XENOVORANS LB400 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Dhindwal, S. / Gomez-Gil, L. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aeu.cif.gz | 496 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aeu.ent.gz | 408.4 KB | Display | PDB format |
PDBx/mmJSON format | 5aeu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aeu ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aeu | HTTPS FTP |
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-Related structure data
Related structure data | 5aewC 2xr8S 5aev C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) BURKHOLDERIA XENOVORANS LB400 (bacteria) Variant: II9 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P37333, biphenyl 2,3-dioxygenase #2: Protein | Mass: 22113.846 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS LB400 (bacteria) Variant: II9 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P37334, biphenyl 2,3-dioxygenase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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