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Yorodumi- PDB-1mpy: STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mpy | ||||||
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Title | STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2 | ||||||
Components | CATECHOL 2,3-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / CATECHOL 2 / 3-DIOXYGENASE / EXTRADIOL DIOXYGENASE / NON HEME IRON DIOXYGENASE / METAPYROCATECHASE | ||||||
Function / homology | Function and homology information catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / toluene catabolic process / ferrous iron binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Kita, A. / Kita, S. / Fujisawa, I. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2. Authors: Kita, A. / Kita, S. / Fujisawa, I. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K. #1: Journal: J.Biochem.(Tokyo) / Year: 1997 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Expressed Pseudomonas Putida Catechol 2,3-Dioxygenase Authors: Kita, A. / Kita, S. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mpy.cif.gz | 241.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mpy.ent.gz | 195.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/1mpy ftp://data.pdbj.org/pub/pdb/validation_reports/mp/1mpy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35203.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: FE(II) FORM / Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: MT-2 / Gene: XYLE / Plasmid: PHT3 / Species (production host): Escherichia coli / Gene (production host): XYLE Production host: Escherichia coli str. K12 substr. W3110 (bacteria) Strain (production host): W3110 / References: UniProt: P06622, catechol 2,3-dioxygenase #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-ACN / #4: Water | ChemComp-HOH / | Nonpolymer details | RESIDUE 309S ARE ACETONE MOLECULES ASSIGNED TO THE APPROPRIATE DENSITY FEATURES. ACETONE IS ...RESIDUE 309S ARE ACETONE MOLECULES ASSIGNED TO THE APPROPRIAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Kita, A., (1997) J.Biochem.(Tokyo), 122, 201. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Detector: FILM |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 46225 / % possible obs: 86 % / Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 14.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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