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- PDB-1nbh: Structure of glycine N-methyltransferase complexed with S-adenosy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nbh | ||||||
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Title | Structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace | ||||||
![]() | Glycine N-methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase / Glycine N-methyltransferase / S-adenosylmethionine / Enzyme catalytic mechanism | ||||||
Function / homology | ![]() selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / glycine N-methyltransferase activity / sarcosine metabolic process / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process ...selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / glycine N-methyltransferase activity / sarcosine metabolic process / methyltransferase complex / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / folic acid binding / glycine binding / regulation of gluconeogenesis / glycogen metabolic process / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Takata, Y. / Takusagawa, F. | ||||||
![]() | ![]() Title: Catalytic mechanism of glycine N-methyltransferase Authors: Takata, Y. / Huang, Y. / Komoto, J. / Yamada, T. / Konishi, K. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.5 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 581.8 KB | Display | ![]() |
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Full document | ![]() | 634.7 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 32460.830 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SAM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 3400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 10, 2002 / Details: Confocal optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→10 Å / Num. obs: 37008 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.8→3 Å / % possible all: 81 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 36870 / % possible obs: 99 % / Num. measured all: 195411 |
Reflection shell | *PLUS Lowest resolution: 2.9 Å / % possible obs: 97 % / Rmerge(I) obs: 0.258 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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