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- PDB-4paa: Crystal structure of the mature form of rat DMGDH complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4paa | ||||||
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Title | Crystal structure of the mature form of rat DMGDH complexed with tetrahydrofolate | ||||||
![]() | Dimethylglycine dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / dimethylglycine dehydrogenase / rat / tetrahydrofolate | ||||||
Function / homology | ![]() dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / tetrahydrofolate interconversion / folic acid binding / choline metabolic process / flavin adenine dinucleotide binding / oxidoreductase activity ...dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / tetrahydrofolate interconversion / folic acid binding / choline metabolic process / flavin adenine dinucleotide binding / oxidoreductase activity / mitochondrial matrix / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Authors: Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342.6 KB | Display | ![]() |
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PDB format | ![]() | 268.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 57.2 KB | Display | |
Data in CIF | ![]() | 79.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4p9sC ![]() 4pabC ![]() 1pj5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 38 - 853 / Label seq-ID: 19 - 834
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Components
#1: Protein | Mass: 95204.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5RKL4, UniProt: Q63342*PLUS, dimethylglycine dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M K/Na-tartrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. all: 87235 / Num. obs: 87235 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.061 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 1.9 / % possible all: 90.6 |
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Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 1PJ5 Resolution: 2.26→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.875 / SU B: 8.928 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.719 Å2
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Refinement step | Cycle: 1 / Resolution: 2.26→40 Å
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Refine LS restraints |
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