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Yorodumi- PDB-8ix6: Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Bradyrh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ix6 | |||||||||
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Title | Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Bradyrhizobium sp. WSM3983 | |||||||||
Components | Aldolase | |||||||||
Keywords | OXIDOREDUCTASE / class II aldolase-like / dioxygenase / non-heme iron / His-triad | |||||||||
Function / homology | NICKEL (II) ION Function and homology information | |||||||||
Biological species | Bradyrhizobium sp. WSM3983 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å | |||||||||
Authors | Tsujino, S. / Yamada, Y. / Fujiwara, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ix6.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ix6.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ix6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ix6_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 8ix6_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 8ix6_validation.xml.gz | 10 KB | Display | |
Data in CIF | 8ix6_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/8ix6 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ix6 | HTTPS FTP |
-Related structure data
Related structure data | 8il8C 8iqaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29502.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. WSM3983 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||
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#2: Chemical | ChemComp-NI / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.56M ammonium sulfate, 25% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→76.95 Å / Num. obs: 11546 / % possible obs: 100 % / Redundancy: 38.1 % / Biso Wilson estimate: 60.18 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 2.47→2.51 Å / Rmerge(I) obs: 1.766 / Num. unique obs: 569 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.47→76.95 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2428 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.13 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→76.95 Å
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Refine LS restraints |
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LS refinement shell |
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