+Open data
-Basic information
Entry | Database: PDB / ID: 1kw8 | |||||||||
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Title | Crystal structure of BphC-2,3-dihydroxybiphenyl-NO complex | |||||||||
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: 2 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 | 1kw8.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kw8.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kw8 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kw8 | 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 octamer 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-NO / |
#4: Chemical | ChemComp-BPY / |
#5: 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: 3.14 Å3/Da / Density % sol: 60.8 % | |||||||||||||||||||||||||
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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: 2→87.71 Å / Num. all: 27911 / Num. obs: 27911 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.324 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 87.7 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→87.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.511 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.113 / 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: 19.963 Å2
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Refinement step | Cycle: LAST / Resolution: 2→87.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 87.7 Å / Rfactor Rfree: 0.184 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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