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Yorodumi- PDB-4h2p: Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h2p | ||||||
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Title | Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) | ||||||
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: 1.981 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 | 4h2p.cif.gz | 350.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h2p.ent.gz | 283.5 KB | Display | PDB format |
PDBx/mmJSON format | 4h2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h2p ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h2p | HTTPS FTP |
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-Related structure data
Related structure data | 3aljC 3allC 3almC 4gf7C 4h2nC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41798.488 Da / Num. of mol.: 4 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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-Non-polymers , 8 types, 1476 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 4.21 Å3/Da / Density % sol: 70.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.0M Lithium sulfate, 6% PEG 8000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: 1.98→50 Å / Num. obs: 195890 / % possible obs: 98.7 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 7.8 / Num. unique all: 9302 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GMB Resolution: 1.981→43.905 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.19 / σ(F): 1.33 / Phase error: 18.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.303 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.13 Å2 / Biso mean: 24.8726 Å2 / Biso min: 8.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.981→43.905 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: 30
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