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Yorodumi- PDB-2xso: CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xso | ||||||
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Title | CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 | ||||||
Components |
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Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 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 | BURKHOLDERIA XENOVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kumar, P. / Bolin, J.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xso.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2xso.ent.gz | 2.4 MB | Display | PDB format |
PDBx/mmJSON format | 2xso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xso_validation.pdf.gz | 675 KB | Display | wwPDB validaton report |
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Full document | 2xso_full_validation.pdf.gz | 814.5 KB | Display | |
Data in XML | 2xso_validation.xml.gz | 278.5 KB | Display | |
Data in CIF | 2xso_validation.cif.gz | 383.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xso ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xso | HTTPS FTP |
-Related structure data
Related structure data | 2xr8SC 2xrxC 2xshC 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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1 |
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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.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: P4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37333, biphenyl 2,3-dioxygenase #2: Protein | Mass: 22113.846 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: P4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37334, biphenyl 2,3-dioxygenase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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