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Yorodumi- PDB-5y6q: Crystal structure of an aldehyde oxidase from Methylobacillus sp.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y6q | ||||||
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Title | Crystal structure of an aldehyde oxidase from Methylobacillus sp. KY4400 | ||||||
Components | (Aldehyde oxidase ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / aldehyde oxidase molybdenum enzyme Methylobacillus sp. KY4400 | ||||||
Function / homology | Function and homology information FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Methylobacillus sp. KY4400 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mikami, B. / Uchida, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J. Biochem. / Year: 2018 Title: Crystal structure of an aldehyde oxidase from Methylobacillus sp. KY4400. Authors: Uchida, H. / Mikami, B. / Yamane-Tanabe, A. / Ito, A. / Hirano, K. / Oki, M. #1: Journal: Biosci. Biotechnol. Biochem. / Year: 2005 Title: Cloning and sequencing of the aldehyde oxidase gene from Methylobacillus sp. KY4400. Authors: Yasuhara, A. / Akiba-Goto, M. / Aisaka, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y6q.cif.gz | 269.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y6q.ent.gz | 207.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y6q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5y6q_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5y6q_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 5y6q_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/5y6q ftp://data.pdbj.org/pub/pdb/validation_reports/y6/5y6q | HTTPS FTP |
-Related structure data
Related structure data | 5g5hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Aldehyde oxidase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 17311.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus sp. KY4400 (bacteria) / Gene: aoms / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q84IY0 |
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#2: Protein | Mass: 35616.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus sp. KY4400 (bacteria) / Gene: aomm / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q84IX9 |
#3: Protein | Mass: 83153.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus sp. KY4400 (bacteria) / Gene: aoml / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q84IX8 |
-Non-polymers , 9 types, 533 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-FAD / | #7: Chemical | ChemComp-SF4 / | #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-MOS / | #10: Chemical | ChemComp-MCN / | #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Sequence details | The depositors state that the database UNP codes Q84IY0/Q84IX9 are incorrect at these positions. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Sodium citrate buffer, pH 5.5, 4-5% W/V isopropanol, 22-27% W/V PEG 4000, 10-16% W/V ammonium sulfate, red cubic flash cooled after brief soaking to the bottom solution containing 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 44006 / % possible obs: 99.1 % / Redundancy: 15.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.022 / Χ2: 0.856 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 1944 / CC1/2: 0.901 / Rpim(I) all: 0.161 / Χ2: 0.487 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G5H Resolution: 2.5→46.116 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.116 Å
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Refine LS restraints |
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LS refinement shell |
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