+Open data
-Basic information
Entry | Database: PDB / ID: 1p1b | ||||||
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Title | Guanidinoacetate methyltransferase | ||||||
Components | Guanidinoacetate N-methyltransferase | ||||||
Keywords | TRANSFERASE / Guanidinoacetate methyltransferase / Methyltransferase / S-adenosylhomocysteine | ||||||
Function / homology | Function and homology information 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 ...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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Komoto, J. / Takusagawa, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p1b.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p1b.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/1p1b ftp://data.pdbj.org/pub/pdb/validation_reports/p1/1p1b | HTTPS FTP |
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-Related structure data
-Links
-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.) Rattus norvegicus (Norway rat) / Gene: GAMT / Production host: Escherichia coli (E. coli) References: UniProt: P10868, guanidinoacetate N-methyltransferase #2: Chemical | ChemComp-SAH / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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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 |