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- PDB-1pj6: Crystal structure of dimethylglycine oxidase of Arthrobacter glob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pj6 | ||||||
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Title | Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid | ||||||
![]() | N,N-dimethylglycine oxidase | ||||||
![]() | OXIDOREDUCTASE / channelling / folate binding / FAD binding / amine oxidation | ||||||
Function / homology | ![]() dimethylglycine oxidase / dimethylglycine oxidase activity / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leys, D. / Basran, J. / Scrutton, N.S. | ||||||
![]() | ![]() Title: Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase. Authors: Leys, D. / Basran, J. / Scrutton, N.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.7 KB | Display | ![]() |
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PDB format | ![]() | 164.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 988.2 KB | Display | ![]() |
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Full document | ![]() | 996.4 KB | Display | |
Data in XML | ![]() | 47.2 KB | Display | |
Data in CIF | ![]() | 77.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pj5SC ![]() 1pj7C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | DMGO is a tetramer (dimer of dimers) formed by applying the 222 point symmetry of the C222 spacegroup |
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Components
#1: Protein | Mass: 90075.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-FOL / |
#4: Chemical | ChemComp-FAD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG 2000MME, 0.2 MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2002 |
Radiation | Monochromator: sychrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→15 Å / Num. all: 106504 / Num. obs: 106504 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.65→1.7 Å / % possible all: 99 |
Reflection shell | *PLUS Lowest resolution: 1.7 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PJ5 Resolution: 1.65→14.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.568 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.253 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→14.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.193 / Rfactor Rwork: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |