[English] 日本語
Yorodumi- PDB-3gmc: Crystal Structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid Oxygenase with substrate bound | ||||||
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 / MOLECULAR REPLACEMENT / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gmc.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gmc.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmc ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmc | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45739.816 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: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 6-9% PEG8000, 100 mM Tris, 10 mM soak with MHPC, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 58150 / % possible obs: 94.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Χ2: 0.915 / Net I/σ(I): 12.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.04 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 49741 / 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
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.769 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.42 Å2 / Biso mean: 23.39 Å2 / Biso min: 9.23 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.04 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|