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Yorodumi- PDB-1lkd: CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lkd | ||||||
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Title | CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB) | ||||||
Components | BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / Extradiol dioxygenase / 2 / 3-Dihydroxybiphenyl / non-heme iron / Anaerobic / PCB biodegradation | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dai, S. / Bolin, J.T. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Identification and analysis of a bottleneck in PCB biodegradation Authors: Dai, S. / Vaillancourt, F.H. / Maaroufi, H. / Drouin, N.M. / Neau, D.B. / Snieckus, V. / 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 | 1lkd.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lkd.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lkd ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lkd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Burkholderia xenovorans (bacteria) / Strain: LB400 Description: Burkholderia sp. strain LB400 has been reclassifed. Prior publications may refer to this organism as pseudomonas sp. Strain LB400 or burkholderia cepacia strain LB400. See M.G.Fain,J.D. ...Description: Burkholderia sp. strain LB400 has been reclassifed. Prior publications may refer to this organism as pseudomonas sp. Strain LB400 or burkholderia cepacia strain LB400. See M.G.Fain,J.D.Haddock, Current Microbiol. (2001) 42:269-73 Plasmid: pLEBD4 / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442 References: UniProt: P47228, biphenyl-2,3-diol 1,2-dioxygenase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-P6G / | #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: 3.1 Å3/Da / Density % sol: 60 % | |||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 400, t-Butanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K | |||||||||||||||
Crystal grow | *PLUS Temperature: 5-10 ℃ / Method: vapor diffusion / Details: Han, S., (1995) Science, 270, 976. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97833 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 10, 2001 |
Radiation | Monochromator: SAGITALLY FOCUSED Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97833 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. all: 46029 / Num. obs: 46029 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 1.69→1.75 Å / Rmerge(I) obs: 0.409 / % possible all: 73.7 |
Reflection | *PLUS Num. measured all: 2212442 |
Reflection shell | *PLUS % possible obs: 73.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2808076.19 / Data cutoff high rms absF: 2808076.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3977 Å2 / ksol: 0.413408 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.2 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.212 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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