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Open data
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Basic information
Entry | Database: PDB / ID: 3orh | |||||||||
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Title | Human guanidinoacetate N-methyltransferase with SAH | |||||||||
![]() | Guanidinoacetate N-methyltransferase | |||||||||
![]() | TRANSFERASE / GUANIDINOACETATE N-METHYLTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | ![]() guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / Transcriptional Regulation by MECP2 / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / methyltransferase activity / muscle contraction ...guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / Transcriptional Regulation by MECP2 / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / methyltransferase activity / muscle contraction / animal organ morphogenesis / methylation / spermatogenesis / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dong, A. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() Title: The crystal structure of human guanidinoacetate N-methyltransferase with SAH Authors: Wu, H. / Dong, A. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.1 KB | Display | ![]() |
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PDB format | ![]() | 169.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 65.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xclS 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. |
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Components
#1: Protein | Mass: 26347.123 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q14353, 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: 2.86 Å3/Da / Density % sol: 57.01 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 6.5 Details: 21% PEG3350, 0.1M CACL2, 0.1M TRIS, 1MM GUANIDINE HCL, pH 6.5, VAPOR DIFFUSION, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2005 / Details: SI(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→37.2 Å / Num. all: 97258 / Num. obs: 97258 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.7 / Rsym value: 0.7 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3582 / % possible all: 74 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1XCL Resolution: 1.86→37.2 Å / Cor.coef. Fo:Fc: 0.9154 / Cor.coef. Fo:Fc free: 0.8976 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso max: 207.74 Å2 / Biso mean: 24.6722 Å2 / Biso min: 8.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.234 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→37.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 Å / Total num. of bins used: 20
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