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Yorodumi- PDB-1bdb: CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bdb | ||||||
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Title | CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400 | ||||||
Components | CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NAD-DEPENDENT OXIDOREDUCTASE / SHORT-CHAIN ALCOHOL DEHYDROGENASE / PCB DEGRADATION | ||||||
Function / homology | Function and homology information cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity / : Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Huelsmeyer, M. / Hecht, H.-J. / Niefind, K. / Hofer, B. / Timmis, K.N. / Schomburg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution. Authors: Hulsmeyer, M. / Hecht, H.J. / Niefind, K. / Hofer, B. / Eltis, L.D. / Timmis, K.N. / Schomburg, D. #1: Journal: Gene / Year: 1993 Title: Genetic Analysis of a Pseudomonas Locus Encoding a Pathway for Biphenyl/Polychlorinated Biphenyl Degradation Authors: Hofer, B. / Eltis, L.D. / Dowling, D.N. / Timmis, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bdb.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bdb.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bdb_validation.pdf.gz | 765.5 KB | Display | wwPDB validaton report |
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Full document | 1bdb_full_validation.pdf.gz | 770.6 KB | Display | |
Data in XML | 1bdb_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1bdb_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/1bdb ftp://data.pdbj.org/pub/pdb/validation_reports/bd/1bdb | HTTPS FTP |
-Related structure data
Related structure data | 2hsdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28929.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. (bacteria) / Cellular location: CYTOPLASM / Variant: PLEBD4 / Strain: LB400 / References: UniProt: P47227 |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M CITRATE/PHOSPHATE BUFFER, PH 7.5, 1.2 M AMMONIUM SULFATE CONTAINING 50 MM NAD | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 18861 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.067 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 14.4 / Rsym value: 0.188 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 19980 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Lowest resolution: 2.08 Å / % possible obs: 94 % / Rmerge(I) obs: 0.188 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HSD Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 17.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 18861 / Rfactor all: 0.179 / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |