[English] 日本語
Yorodumi- PDB-1lgt: CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lgt | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2'-Cl 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lgt.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lgt.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lgt_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lgt_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 1lgt_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1lgt_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/1lgt ftp://data.pdbj.org/pub/pdb/validation_reports/lg/1lgt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 8||||||||
Unit cell |
|
-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 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 400, t-Butanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||
Crystal grow | *PLUS Temperature: 5-10 ℃ / Method: vapor diffusion / Details: Han, S., (1995) Science, 270, 976. | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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(111) / 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: 84926 / Num. obs: 84926 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 1.69→1.75 Å / Rmerge(I) obs: 0.34 / % possible all: 96.7 |
Reflection | *PLUS Num. obs: 44042 / % possible obs: 96.8 % / Num. measured all: 1480972 |
Reflection shell | *PLUS % possible obs: 94.8 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2522232.85 / Data cutoff high rms absF: 2522232.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Solvents 8036, 9204 and 9206 mark density features that may be associated with a partially occupied PEG molecule from the crystallization.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.2451 Å2 / ksol: 0.391747 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|