+Open data
-Basic information
Entry | Database: PDB / ID: 1eiq | ||||||
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Title | 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE | ||||||
Components | 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / four repetitions of beta-alpha-beta-beta-beta motifs | ||||||
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 | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Senda, T. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2001 Title: Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase. Authors: Uragami, Y. / Senda, T. / Sugimoto, K. / Sato, N. / Nagarajan, V. / Masai, E. / Fukuda, M. / Mitsu, Y. #1: Journal: PROC.JPN.ACAD.,SER.B / Year: 1995 Title: Three-dimensional Structure of 2,3-dihydroxybiphenyl dioxygenase (BphC enzyme) from Pseudomonas sp. strain KKS102 having Polychlorinated Biphenyl (PCB) Degrading Activity. Authors: Sugiyama, K. / Senda, T. / Kimbara, K. / Fukuda, M. / Mitsui, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eiq.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eiq.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/1eiq ftp://data.pdbj.org/pub/pdb/validation_reports/ei/1eiq | 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: 32151.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: KKS102 / Plasmid: PHNA2 / Production host: Escherichia coli (E. coli) References: UniProt: P17297, biphenyl-2,3-diol 1,2-dioxygenase |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Compound details | Substrate free form. Structure determined under aerobic condition (inactive form structure) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.84 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / pH: 7.5 Details: 285K, Tris/HCl, Ammonium sulfate, hexylene glycol, pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / Method: batch method | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 28, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→60 Å / Num. all: 27236 / Num. obs: 25056 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.98→2.25 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.201 / % possible all: 83.5 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 24620 / % possible obs: 88.1 % |
Reflection shell | *PLUS % possible obs: 83.5 % |
-Processing
Software |
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Refinement | Resolution: 2→60 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→60 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 24620 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.194 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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