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- PDB-1knd: Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Comple... -
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Open data
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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 | ||||||
![]() | 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / dioxygenase / 2 / 3-dihydroxybiphenyl / catechol | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Han, S. / Bolin, J.T. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: 2,3-Dihydroxybiphenyl 1,2-dioxygenase. Authors: Bolin, J.T. / Eltis, L.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 53.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kmyC ![]() 1knfC ![]() 1hanS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 |
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Components
#1: Protein | Mass: 32377.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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: ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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