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- PDB-1mpy: STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mpy | ||||||
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Title | STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2 | ||||||
![]() | CATECHOL 2,3-DIOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / CATECHOL 2 / 3-DIOXYGENASE / EXTRADIOL DIOXYGENASE / NON HEME IRON DIOXYGENASE / METAPYROCATECHASE | ||||||
Function / homology | ![]() catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / toluene catabolic process / ferrous iron binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kita, A. / Kita, S. / Fujisawa, I. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.7 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407 KB | Display | ![]() |
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Full document | ![]() | 440.7 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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