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Yorodumi- PDB-2yfj: Crystal structure of Biphenyl dioxygenase variant RR41 with diben... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yfj | ||||||
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Title | Crystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran | ||||||
Components | (BIPHENYL DIOXYGENASE SUBUNIT ...) x 2 | ||||||
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: 2.15 Å | ||||||
Authors | Kumar, P. / Sylvestre, M. / Bolin, J.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Retuning Rieske-Type Oxygenases to Expand Substrate Range. Authors: Mohammadi, M. / Viger, J. / Kumar, P. / Barriault, 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 | 2yfj.cif.gz | 717.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yfj.ent.gz | 589 KB | Display | PDB format |
PDBx/mmJSON format | 2yfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yfj_validation.pdf.gz | 492.7 KB | Display | wwPDB validaton report |
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Full document | 2yfj_full_validation.pdf.gz | 511.3 KB | Display | |
Data in XML | 2yfj_validation.xml.gz | 68.2 KB | Display | |
Data in CIF | 2yfj_validation.cif.gz | 106.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/2yfj ftp://data.pdbj.org/pub/pdb/validation_reports/yf/2yfj | HTTPS FTP |
-Related structure data
Related structure data | 2yfiC 2xr8S S: Starting model for refinement C: citing same article (ref.) |
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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, 667 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 6 / Details: PEG 5000 MME AND 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 MX-300 / 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: 2.1→100 Å / Num. obs: 210175 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.02 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XR8 Resolution: 2.15→138.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.747 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.21 / 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: 42.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→138.68 Å
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Refine LS restraints |
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