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Yorodumi- PDB-5hxi: 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5HN bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hxi | ||||||
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Title | 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5HN bound | ||||||
Components | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta fold / flavoenzyme / substrate complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kobayashi, J. / Mikami, B. | ||||||
Citation | Journal: J. Biosci. Bioeng. / Year: 2017 Title: Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti Authors: Kobayashi, J. / Yoshida, H. / Yagi, T. / Kamitori, S. / Hayashi, H. / Mizutani, K. / Takahashi, N. / Mikami, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hxi.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hxi.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 5hxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hxi_validation.pdf.gz | 746.3 KB | Display | wwPDB validaton report |
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Full document | 5hxi_full_validation.pdf.gz | 749.6 KB | Display | |
Data in XML | 5hxi_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 5hxi_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/5hxi ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hxi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41798.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium loti (strain MAFF303099) (bacteria) Strain: MAFF303099 / Gene: mlr6788 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q988D3 |
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-Non-polymers , 7 types, 486 molecules
#2: Chemical | ChemComp-FAD / | ||||||
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#3: Chemical | ChemComp-BME / | ||||||
#4: Chemical | ChemComp-5HN / | ||||||
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8% PEG8000, 0.1M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→93.13 Å / Num. all: 68494 / Num. obs: 68494 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.379 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.097 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.594 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50 Å
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Refine LS restraints |
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