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Yorodumi- PDB-2yfl: Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yfl | ||||||
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Title | Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran | ||||||
Components | (BIPHENYL DIOXYGENASE SUBUNIT ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / DEGRADATION / BPDO | ||||||
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: 2.6 Å | ||||||
Authors | Kumar, P. / Bolin, J.T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2012 Title: Structural Insights Into the Metabolism of 2-Chlorodibenzofuran by an Evolved Biphenyl Dioxygenase. Authors: Kumar, P. / Mohammadi, M. / Dhindwal, S. / Pham, T.T. / 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 | 2yfl.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2yfl.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2yfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yfl_validation.pdf.gz | 564.4 KB | Display | wwPDB validaton report |
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Full document | 2yfl_full_validation.pdf.gz | 609.5 KB | Display | |
Data in XML | 2yfl_validation.xml.gz | 125.7 KB | Display | |
Data in CIF | 2yfl_validation.cif.gz | 170.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/2yfl ftp://data.pdbj.org/pub/pdb/validation_reports/yf/2yfl | HTTPS FTP |
-Related structure data
Related structure data | 2xr8S 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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Unit cell |
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-Components
-BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 51562.398 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: RR41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37333, biphenyl 2,3-dioxygenase #2: Protein | Mass: 22113.846 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Variant: RR41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37334, biphenyl 2,3-dioxygenase |
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-Non-polymers , 4 types, 368 molecules
#3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FE2 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.22 Å3/Da / Density % sol: 44.72 % / Description: NONE |
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Crystal grow | pH: 6 / Details: PEG 5000, PIPES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 97588 / % possible obs: 80 % / Observed criterion σ(I): 1.5 / Redundancy: 3.1 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 49.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XR8 Resolution: 2.6→137.36 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.88 / SU B: 35.906 / SU ML: 0.372 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.448 / 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: 68.641 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→137.36 Å
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Refine LS restraints |
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