+Open data
-Basic information
Entry | Database: PDB / ID: 4h2n | |||||||||
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Title | Crystal structure of MHPCO, Y270F mutant | |||||||||
Components | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | |||||||||
Keywords | OXIDOREDUCTASE / FAD-binding motif / Oxygenase / FAD / 3-hydroxypyridine-5-carboxylic acid | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Rhizobium loti (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å | |||||||||
Authors | Kobayashi, J. / Yoshida, H. / Mikami, B. / Hayashi, H. / 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. / Mikami, B. / Hayashi, H. / 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 | 4h2n.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h2n.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 4h2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h2n ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h2n | HTTPS FTP |
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-Related structure data
Related structure data | 3aljC 3allC 3almC 4gf7C 4h2pC 4jy2C 4jy3C 3gmbS 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
#1: Protein | Mass: 41782.488 Da / Num. of mol.: 1 / Mutation: Y270F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6788 / 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 | ChemComp-BME / |
#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: 2.58 Å3/Da / Density % sol: 52.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.5, 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: May 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 18939 / % possible obs: 96.5 % / Redundancy: 7 % / Biso Wilson estimate: 29.31 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 4.8 / Num. unique all: 968 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GMB Resolution: 2.302→37.978 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.71 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.96 Å2 / Biso mean: 33.5164 Å2 / Biso min: 17.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.302→37.978 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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