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Yorodumi- PDB-1kw9: Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kw9 | ||||||||||||
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Title | Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution | ||||||||||||
Components | 2,3-Dihydroxybiphenyl dioxygenase | ||||||||||||
Keywords | OXIDOREDUCTASE / four time repetitions of the beta-alpha-beta-beta-beta motif | ||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | Sato, N. / Uragami, Y. / Nishizaki, T. / Takahashi, Y. / Sazaki, G. / Sugimoto, K. / Nonaka, T. / Masai, E. / Fukuda, M. / Senda, T. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase Authors: Sato, N. / Uragami, Y. / Nishizaki, T. / Takahashi, Y. / Sazaki, G. / Sugimoto, K. / Nonaka, T. / Masai, E. / Fukuda, M. / Senda, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kw9.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kw9.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kw9 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kw9 | 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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Details | The biological assembly is a octemer generated from the monomer in the asymmetric unit by the operations: x, y, z; .1-x, 1-y, z; 1-x, y, -z; x, 1-y, -z; y, x, -z; 1-y, 1-x, -z; 1-y, x, z; y, 1-x, z; |
-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 / Production host: Escherichia coli (E. coli) References: UniProt: P17297, biphenyl-2,3-diol 1,2-dioxygenase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-BPY / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.65 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: batch / pH: 7.5 Details: Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / Method: batch method / Details: Uragami, Y., (2001) J.Inorg.Biochem., 83, 269. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2000 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.939→28.67 Å / Num. all: 28896 / Num. obs: 28532 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.94→2.04 Å / % possible all: 93.5 |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 84.5 Å / Redundancy: 12 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→84.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.412 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.174 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→84.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.945→1.995 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 84.5 Å / Rfactor Rfree: 0.183 / Rfactor Rwork: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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