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Yorodumi- PDB-3alj: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3alj | ||||||
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Title | Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, reduced form | ||||||
Components | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Kobayashi, J. / Yoshida, H. / Yoshikane, Y. / Kamitori, S. / Yagi, T. | ||||||
Citation | Journal: To be Published Title: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase Authors: Kobayashi, J. / Yoshida, H. / Yoshikane, Y. / Kamitori, S. / Yagi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3alj.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3alj.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 3alj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3alj ftp://data.pdbj.org/pub/pdb/validation_reports/al/3alj | HTTPS FTP |
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-Related structure data
Related structure data | 3allC 3almC 4gf7C 4h2nC 4h2pC 4jy2C 4jy3C 3alh C: citing same article (ref.) 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 on special symmetry positions |
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Details | Biological unit is tetramer, but specific interaction was not observed. |
-Components
#1: Protein | Mass: 41798.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: co-expression with chaperonine GroEL,ES / Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6788 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988D3, EC: 1.14.12.4 | ||||
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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.54 Å3/Da / Density % sol: 51.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris-HCl pH 8.5, 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2009 |
Radiation | Monochromator: Si-single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. all: 70553 / Num. obs: 70553 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.363 / Num. unique all: 3470 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ALH 3alh Resolution: 1.48→29.63 Å / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 14.137 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→29.63 Å
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Refine LS restraints |
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LS refinement shell |
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