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Yorodumi- PDB-1knd: Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1knd | ||||||
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Title | Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with Catechol under Anaerobic Condition | ||||||
Components | 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / 2 / 3-dihydroxybiphenyl / 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 | 1knd.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1knd.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1knd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knd ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knd | HTTPS FTP |
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-Related structure data
Related structure data | 1kmyC 1knfC 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 | 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-CAQ / | #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, 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 23, 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→30 Å / Num. all: 32091 / Num. obs: 32091 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / 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 THE SUBSTRATE CATECHOL (CAQ 301) AND WATERS 9001 and 9002 AT 50% OCCUPANCY. ATOMS O3 AND O4 OF CAQ 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: 23.2 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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