[English] 日本語
Yorodumi- PDB-1han: CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1han | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD | ||||||
Components | 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE (OXYGENASE) / EXTRADIOL DIOXYGENASE | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Han, S. / Bolin, J.T. | ||||||
Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Purification and Crystallization of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase Authors: Eltis, L.D. / Hofmann, B. / Hecht, H.-J. / Lunsdorf, H. / Timmis, K.N. | ||||||
History |
| ||||||
Remark 650 | HELIX HELIX DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION ...HELIX HELIX DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION AND MODIFICATION BY VISUAL INSPECTION. | ||||||
Remark 700 | SHEET SHEET DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION ...SHEET SHEET DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED IN PROCHECK WITH CONFIRMATION AND MODIFICATION BY VISUAL INSPECTION. SHEET_ID: N; STRANDS ARE LABELED F,G,H,E,A,D,C,B IN PUBLICATIONS. SHEET_ID: C; STRANDS ARE LABELED R,N,O,P,M,I,L,K,J,Q IN PUBLICATIONS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1han.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1han.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1han.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1han_validation.pdf.gz | 367 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1han_full_validation.pdf.gz | 367.1 KB | Display | |
Data in XML | 1han_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1han_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/1han ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1han | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 8||||||||
Unit cell |
| ||||||||
Details | SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 2 .. 8038 THE ENZYME IS AN OCTAMER IN SOLUTION. THE DISTRIBUTED COORDINATES ARE FOR A MONOMER BELONGING TO AN OCTAMER AT FRACTIONAL COORDINATES (0.0,0.0,0.5), WHICH IS A SITE OF 422 (D4) POINT SYMMETRY. APPLY THE FOLLOWING SEVEN OPERATIONS TO ALL ATOMS IN THIS ENTRY TO GENERATE THE OTHER SUBUNITS IN THIS OCTAMER. SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 2 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 3 0.000000 -1.000000 0.000000 0.00000 SYMMETRY2 3 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 4 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 4 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 4 0.000000 0.000000 -1.000000 111.36000 SYMMETRY1 5 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 5 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 5 0.000000 0.000000 -1.000000 111.36000 SYMMETRY1 6 0.000000 -1.000000 0.000000 0.00000 SYMMETRY2 6 -1.000000 0.000000 0.000000 0.00000 SYMMETRY3 6 0.000000 0.000000 -1.000000 111.36000 SYMMETRY1 7 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 7 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 7 0.000000 0.000000 -1.000000 111.36000 |
-Components
#1: Protein | Mass: 32377.598 Da / Num. of mol.: 1 / Mutation: WILD-TYPE Source method: isolated from a genetically manipulated source Details: FE(II) FORM UNDER ANAEROBIC CONDITIONS / Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Description: HYPEREXPRESSED IN THE PARENT STRAIN / Gene: BPHC / Plasmid: PLEBD4 / Gene (production host): BPHC / Production host: Burkholderia cepacia (bacteria) References: UniProt: P47228, biphenyl-2,3-diol 1,2-dioxygenase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-TBU / | #4: Water | ChemComp-HOH / | Nonpolymer details | RESIDUE 501 IS AN ADVENTITIOUS FE ATOM PRESENT WITH PARTIAL OCCUPANCY ONLY WHEN THE CRYSTAL ...RESIDUE 501 IS AN ADVENTITIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.91 % Description: MWPC DATA WERE USED IN STRUCTURE DETERMINATION AND INITIAL REFINEMENT. IMAGING PLATE DATA WERE USED IN FINAL REFINEMENT. REDUNDANCY AND MERGING R STATISTICS CITED ABOVE ARE FOR IMAGING ...Description: MWPC DATA WERE USED IN STRUCTURE DETERMINATION AND INITIAL REFINEMENT. IMAGING PLATE DATA WERE USED IN FINAL REFINEMENT. REDUNDANCY AND MERGING R STATISTICS CITED ABOVE ARE FOR IMAGING PLATE DATA FROM ONE CRYSTAL. | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||
Crystal grow | *PLUS Temperature: 5-10 ℃ / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||
Detector |
| ||||||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 33261 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | Highest resolution: 1.9 Å / Redundancy: 4.2 % | ||||||||||||
Reflection | *PLUS Observed criterion σ(I): 3 / Num. measured all: 287451 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS Num. unique obs: 3303 / Num. measured obs: 13817 / Rmerge(I) obs: 0.225 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→7 Å / σ(F): 1 Details: THE SIDE CHAIN OF MET 246 IS NEAR THE ACTIVE SITE FE AND IS DISORDERED BETWEEN TWO MAJOR CONFORMERS. THE ELECTRON DENSITY MAPS SUGGEST THAT SEVERAL ADDITIONAL RESIDUES HAVE TWO OF MORE ...Details: THE SIDE CHAIN OF MET 246 IS NEAR THE ACTIVE SITE FE AND IS DISORDERED BETWEEN TWO MAJOR CONFORMERS. THE ELECTRON DENSITY MAPS SUGGEST THAT SEVERAL ADDITIONAL RESIDUES HAVE TWO OF MORE CONFORMATIONS. IN ALL CASES ONLY ONE CONFORMATION WAS REFINED. SEVERAL SIDE CHAIN ATOMS HAVE BEEN ASSIGNED OCCUPANCIES OF 0.10 TO INDICATE THE PRESENCE OF POOR DENSITY AND UNRELIABLE COORDINATES. THESE OCCUPANCIES WERE NOT REFINED. THE OCCUPANCY OF THE FE(II) ION INCLUDED AS RESIDUE 501 WAS ASSIGNED A VALUE OF 0.5 BASED ON ITS RELATIVE ANOMALOUS DIFFERENCE DENSITY. THIS OCCUPANCY WAS NOT REFINED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|