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Yorodumi- PDB-1knf: Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1knf | ||||||
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Title | Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition | ||||||
Components | 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / 2 / 3-dihydroxybiphenyl / 3-methyl catechol | ||||||
Function / homology | Function and homology information biphenyl-2,3-diol 1,2-dioxygenase / biphenyl-2,3-diol 1,2-dioxygenase activity / : / xenobiotic catabolic process / ferrous iron binding Similarity search - Function | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Han, S. / Bolin, J.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol. Authors: Vaillancourt, F.H. / Han, S. / Fortin, P.D. / Bolin, J.T. / Eltis, L.D. #1: Journal: Science / Year: 1995 Title: Crystal Structure of the Biphenyl-cleaving Extradiol Dioxygenase from a PCB-degrading Pseudomonad. Authors: Han, S. / Eltis, L.D. / Timmis, K.N. / Muchmore, S.W. / Bolin, J.T. #2: Journal: Handbook of Metalloproteins / Year: 2001 Title: 2,3-Dihydroxybiphenyl 1,2-dioxygenase. Authors: Bolin, J.T. / Eltis, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1knf.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1knf.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 1knf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knf ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knf | HTTPS FTP |
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-Related structure data
Related structure data | 1kmyC 1kndC 1hanS 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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Unit cell |
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Details | The biological assembly is homo-octamer generated by crystallographic symmetry |
-Components
#1: Protein | Mass: 32377.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 Description: HYPEREXPRESSED IN THE PARENT STRAIN (This organism has been reclassified. Prior publications may refer to this source as Pseudomonas sp. strain LB400.) Gene: BPHC / Plasmid: PLEBD4 / Production host: Burkholderia cepacia (bacteria) References: UniProt: P47228, biphenyl-2,3-diol 1,2-dioxygenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MBD / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, t-butanol, 3-methyl catechol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 30, 1995 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 32641 / Num. obs: 32641 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.08 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 2397 / Rsym value: 0.27 / % possible all: 73.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HAN Resolution: 1.9→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ALL FE-PROTEIN BOND DISTANCES WERE HARMONICALLY RESTRAINED TO AN EQUILIBRIUM DISTANCE OF 2.2 ANGSTROMS USING A WEAK FORCE CONSTANT OF 10 KCAL/(MOLE X ANGSTROM-SQUARED). BOND LENGTH, BOND ...Details: ALL FE-PROTEIN BOND DISTANCES WERE HARMONICALLY RESTRAINED TO AN EQUILIBRIUM DISTANCE OF 2.2 ANGSTROMS USING A WEAK FORCE CONSTANT OF 10 KCAL/(MOLE X ANGSTROM-SQUARED). BOND LENGTH, BOND ANGLE, AND PLANARITY RESTRAINTS SIMILAR TO THOSE USED FOR AROMATIC SIDE CHAINS WERE APPLIED TO HET GROUP CAQ (CATECHOL). FE-CAQ AND FE-WATER BOND DISTANCES WERE NOT RESTRAINED. THE REFINED MODEL INCLUDES TWO MUTALLY EXCLUSIVE STRUCTURES IN THE VICINITY OF THE ACTIVE SITE. STRUCTURE ONE (labeled with alternate conformation marker A) INCLUDES A SUBSTRATE 3-METHYL-CATECHOL (MBD 301) AND WATERS 9001 and 9002 AT 50% OCCUPANCY. ATOMS OA1 AND OA2 OF MBD 301 AND WATER 9001 ARE COORDINATED TO FE2 500. STRUCTURE TWO (labeled with alternate conformation marker B) INCLUDES ONE MOLECULE OF T-BUTANOL (TBU 600) AND WATERS 3001, 3012, AND 4014 AT 50% OCCUPANCY, AND IS EQUIVALENT TO THE SUBSTRATE-FREE STRUCTURE WHERE WATERS 3001 AND 3012 ARE COORDINATED TO FE2 500.
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Displacement parameters | Biso mean: 24.3 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.93 Å
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