[English] 日本語
Yorodumi- PDB-5aew: Crystal structure of II9 variant of Biphenyl dioxygenase from Bur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aew | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl | ||||||
Components | (BIPHENYL DIOXYGENASE SUBUNIT ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / BIPHENYL DIOXYGENASE / BPHAE-II9 / BIPHENYL / POLYCHLORINATED BIPHENYLS | ||||||
Function / homology | Function and homology information biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / 3-phenylpropionate catabolic process / : / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | BURKHOLDERIA XENOVORANS LB400 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Dhindwal, S. / Gomez-Gil, L. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2016 Title: Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase. Authors: Dhindwal, S. / Gomez-Gil, L. / Neau, D.B. / Pham, T.T.M. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5aew.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5aew.ent.gz | 2.4 MB | Display | PDB format |
PDBx/mmJSON format | 5aew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aew_validation.pdf.gz | 682 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5aew_full_validation.pdf.gz | 797.2 KB | Display | |
Data in XML | 5aew_validation.xml.gz | 290.2 KB | Display | |
Data in CIF | 5aew_validation.cif.gz | 408.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aew ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aew | HTTPS FTP |
-Related structure data
Related structure data | 5aeuC 2xr8S 5aev C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-Components
-BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX
#1: Protein | Mass: 51471.262 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS LB400 (bacteria) Variant: II9 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P37333, biphenyl 2,3-dioxygenase #2: Protein | Mass: 22113.846 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS LB400 (bacteria) Variant: II9 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P37334, biphenyl 2,3-dioxygenase |
---|
-Non-polymers , 4 types, 4050 molecules
#3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FE2 / #5: Chemical | ChemComp-BNL / #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | MUTATION AT RESIDUE T335G, F336I, N338T, I341T |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % / Description: NONE |
---|---|
Crystal grow | pH: 6 Details: PEG8000, 50MM MES PH 6.0, GLYCEROL 6% AND 50MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→129.1 Å / Num. obs: 634861 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.88→23.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XR8 Resolution: 1.88→23.34 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.271 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.014 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→23.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|