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Open data
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Basic information
Entry | Database: PDB / ID: 1p1b | ||||||
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Title | Guanidinoacetate methyltransferase | ||||||
![]() | Guanidinoacetate N-methyltransferase | ||||||
![]() | TRANSFERASE / Guanidinoacetate methyltransferase / Methyltransferase / S-adenosylhomocysteine | ||||||
Function / homology | ![]() protein arginine N5-methyltransferase activity / Creatine metabolism / guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine biosynthetic process / embryonic liver development / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth ...protein arginine N5-methyltransferase activity / Creatine metabolism / guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine biosynthetic process / embryonic liver development / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / animal organ morphogenesis / methylation / spermatogenesis / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Komoto, J. / Takusagawa, F. | ||||||
![]() | ![]() Title: Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics. Authors: Komoto, J. / Takata, Y. / Yamada, T. / Konishi, K. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F. | ||||||
History |
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Remark 999 | SEQUENCE The authors of this entry state that the authors of the original sequence paper (PNAS 85, ...SEQUENCE The authors of this entry state that the authors of the original sequence paper (PNAS 85, 694 (1988)) stated that Glu-119 was incorrect and the correct amino acid residue is Val. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.9 KB | Display | ![]() |
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PDB format | ![]() | 130.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626 KB | Display | ![]() |
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Full document | ![]() | 660.4 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 30.6 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22615.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P10868, guanidinoacetate N-methyltransferase #2: Chemical | ChemComp-SAH / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 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→20 Å / Num. all: 24442 / Num. obs: 24442 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 93.3 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 55 Å / Num. obs: 23416 / % possible obs: 99.4 % / Num. measured all: 122476 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.139 |
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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→8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.287 / Rfactor Rwork: 0.215 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.342 / Rfactor Rwork: 0.269 |