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- PDB-5him: Crystal structure of glycine sarcosine N-methyltransferase from M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5him | ||||||||||||
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Title | Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylhomocysteine and dimethylglycine | ||||||||||||
![]() | Glycine sarcosine N-methyltransferase | ||||||||||||
![]() | TRANSFERASE / S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase) / class I / monomethylation of glycine and sarcosine / rate-limiting enzyme in betaine biosynthesis / betaine-mediated feedback inhibition | ||||||||||||
Function / homology | ![]() glycine N-methyltransferase activity / sarcosine metabolic process / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / glycine binding / regulation of gluconeogenesis / one-carbon metabolic process / methylation / protein homotetramerization ...glycine N-methyltransferase activity / sarcosine metabolic process / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / glycine binding / regulation of gluconeogenesis / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Lee, Y.R. / Lin, T.S. / Lai, S.J. / Liu, M.S. / Lai, M.C. / Chan, N.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Analysis of Glycine Sarcosine N-methyltransferase from Methanohalophilus portucalensis Reveals Mechanistic Insights into the Regulation of Methyltransferase Activity Authors: Lee, Y.R. / Lin, T.S. / Lai, S.J. / Liu, M.S. / Lai, M.C. / Chan, N.L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.4 KB | Display | ![]() |
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PDB format | ![]() | 90.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 718.8 KB | Display | ![]() |
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Full document | ![]() | 718.9 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gwxC ![]() 5h02C ![]() 5hiiC ![]() 5hijC ![]() 5hikC ![]() 5hilC ![]() 1xvaS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32800.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: FDF-1 / Gene: gsmt / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-SAH / | ||
#3: Chemical | ChemComp-DMG / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: Protein solution: GSMT (6.6 mg/ml) in 100 mM TES pH 7.3, 2 M KCl, 1 mM EDTA, 1 mM 2-Mercaptoethanol, 0.1 mM SAH and 0.2 M betaine. Crystallization reagent: 0.1 M Tris-HCl pH 8.5 and 1.5 M ...Details: Protein solution: GSMT (6.6 mg/ml) in 100 mM TES pH 7.3, 2 M KCl, 1 mM EDTA, 1 mM 2-Mercaptoethanol, 0.1 mM SAH and 0.2 M betaine. Crystallization reagent: 0.1 M Tris-HCl pH 8.5 and 1.5 M sodium chloride. SAH and dimethylglycine were soaked into crystals before data collection. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2012 |
Radiation | Monochromator: Horizontally Focusing Single Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.338→30 Å / Num. obs: 17982 / % possible obs: 100 % / Redundancy: 5.9 % / Rsym value: 0.078 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.338→2.42 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XVA Resolution: 2.338→27.529 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.338→27.529 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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