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- PDB-2xr8: Crystal structure of biphenyl dioxygenase from Burkholderia xenov... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xr8 | ||||||
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Title | Crystal structure of biphenyl dioxygenase from Burkholderia xenovorans LB400 | ||||||
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![]() | OXIDOREDUCTASE / DEGRADATION / BPDO | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Bolin, J.T. | ||||||
![]() | ![]() Title: Structural Insight Into the Expanded Pcb-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution. Authors: Kumar, P. / Mohammadi, M. / Viger, J.F. / Barriault, D. / Gomez-Gil, L. / Eltis, L.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 | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 645.2 KB | Display | ![]() |
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Full document | ![]() | 712.6 KB | Display | |
Data in XML | ![]() | 237.6 KB | Display | |
Data in CIF | ![]() | 321.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xrxC ![]() 2xshC ![]() 2xsoC ![]() 3gzyS 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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Unit cell |
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Components
#1: Protein | Mass: 51574.383 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22113.846 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FE2 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC SX-165 / Detector: CCD / Date: Jul 25, 2003 |
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→120 Å / Num. obs: 255418 / % possible obs: 89 % / Observed criterion σ(I): 1.4 / Redundancy: 2.8 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.49→2.6 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.4 / % possible all: 30 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GZY Resolution: 2.49→129.1 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.294 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 1.122 / ESU R Free: 0.335 / 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: 29.197 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→129.1 Å
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Refine LS restraints |
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