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- PDB-8il8: Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcalig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8il8 | |||||||||
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Title | Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcaligenes faecalis | |||||||||
![]() | Aldolase | |||||||||
![]() | OXIDOREDUCTASE / class II aldolase-like / dioxygenase / non-heme iron / His-triad | |||||||||
Function / homology | Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / : / Aldolase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tsujino, S. / Yamada, Y. / Fujiwara, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional analysis of pyruvic oxime dioxygenase, a key enzyme of heterotrophic nitrification Authors: Tsujino, S. / Yamada, Y. / Senda, M. / Senda, T. / Fujiwara, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 372.4 KB | Display | ![]() |
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PDB format | ![]() | 303.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iqaC ![]() 8ix6C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29138.920 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-FE2 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 36% (v/v) PEG 400, 0.2M calcium acetate, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→76.44 Å / Num. obs: 55281 / % possible obs: 93.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.76→1.9 Å / Rmerge(I) obs: 0.565 / Num. unique obs: 2766 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 32.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.769→76.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.84 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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