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Yorodumi- PDB-3vb0: Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vb0 | ||||||
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Title | Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1 | ||||||
Components | Glyoxalase/bleomycin resistance protein/dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / translational non-crystallographic symmetry / hypersymmetry / unusual crystal packing / extradiol dioxygenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingomonas wittichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Koksal, M. / Kumar, P. / Bolin, J.T. | ||||||
Citation | Journal: To be Published Title: Crystal structure of a dibenzofuran-degrading dioxygenase: an unusual spatially heterogeneous crystal with a hypersymmetric intensity distribution Authors: Koksal, M. / Kumar, P. / Fortin, P.D. / Eltis, L.D. / Bolin, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vb0.cif.gz | 229.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vb0.ent.gz | 185.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/3vb0 ftp://data.pdbj.org/pub/pdb/validation_reports/vb/3vb0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 2 - 290 / Label seq-ID: 2 - 290
NCS ensembles :
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-Components
#1: Protein | Mass: 32311.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: pAHD1 is pVLT31 plasmid containing dbfB gene / Source: (gene. exp.) Sphingomonas wittichii (bacteria) / Strain: RW1 / Gene: dbfB, Swit_4902 / Plasmid: pAHD1 / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442 References: UniProt: A5VGW5, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Chemical | ChemComp-FE2 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 1.727 Å3/Da / Density % sol: 28.79 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.4-2.0 M (NH4)2SO4, 2% PEG 400 and 0.1 M PIPES at pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2005 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→92.85 Å / Num. all: 53614 / Num. obs: 51572 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2 / Num. unique all: 4815 / Rsym value: 0.499 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus globerulus strain P6 Resolution: 2.1→92.85 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.582 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.266 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.474 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→92.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.097→2.151 Å / Total num. of bins used: 20
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