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Yorodumi- PDB-3gmb: Crystal Structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmb | ||||||
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Title | Crystal Structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid Oxygenase | ||||||
Components | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | ||||||
Keywords | OXIDOREDUCTASE / flavin monooxygenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | McCulloch, K.M. / Mukherjee, T. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structure of the PLP degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications. Authors: McCulloch, K.M. / Mukherjee, T. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gmb.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gmb.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmb ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 46255.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr6788 / Plasmid: XF1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q988D3 #2: Chemical | #3: 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: 2.96 Å3/Da / Density % sol: 58.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 6-9% PEG8000, 100 mM Tris, pH 8.2, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→76.08 Å / Num. obs: 62559 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / Χ2: 1.852 / Net I/σ(I): 13.906 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→29.89 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2963998 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.894 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.35 Å2 / Biso mean: 19.373 Å2 / Biso min: 4.24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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