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- PDB-2xso: CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURK... -
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Basic information
Entry | Database: PDB / ID: 2xso | ||||||
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Title | CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 | ||||||
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Function / homology | ![]() ![]() ![]() 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 | ![]() | 2.9 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 | ![]() 2xr8SC ![]() 2xrxC ![]() 2xshC 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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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51528.383 Da / Num. of mol.: 12 / Mutation: YES 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 / | ![]() 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: 50 % / Description: NONE |
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Crystal grow![]() | pH: 6 / Details: PEG 8K, PIPES BUFFER PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→125 Å / Num. obs: 377867 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 64.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2XR8 Resolution: 2.2→125 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.185 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.256 / 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: 30.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→125 Å
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Refine LS restraints |
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