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Yorodumi- PDB-1r8x: Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r8x | ||||||
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Title | Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form) | ||||||
Components | glycine N-methyltransferase | ||||||
Keywords | TRANSFERASE / Glycine N-Methyltransferase | ||||||
Function / homology | Function and homology information glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methyltransferase complex / Glyoxylate metabolism and glycine degradation / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding ...glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / methyltransferase complex / Glyoxylate metabolism and glycine degradation / methionine metabolic process / S-adenosylhomocysteine metabolic process / glycine metabolic process / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / glycogen metabolic process / folic acid binding / glycine binding / regulation of gluconeogenesis / S-adenosylmethionine-dependent methyltransferase activity / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Pakhomova, S. / Luka, Z. / Wagner, C. / Newcomer, M.E. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes. Authors: Pakhomova, S. / Luka, Z. / Grohmann, S. / Wagner, C. / Newcomer, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r8x.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r8x.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/1r8x ftp://data.pdbj.org/pub/pdb/validation_reports/r8/1r8x | HTTPS FTP |
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-Related structure data
Related structure data | 1r74C 1r8yC 1xvaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -y,-x,-z+1.5 |
-Components
#1: Protein | Mass: 32587.029 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: GNMT / Plasmid: pET17b, pMME / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QXF8 #2: Chemical | ChemComp-BME / #3: Chemical | #4: 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: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: PEG4000, isopropanol, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 17, 2002 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 14973 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rsym value: 0.068 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.95→3.05 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.431 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XVA Resolution: 2.95→10.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 24.137 / SU ML: 0.427 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.202 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→10.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.95→3.02 Å / Total num. of bins used: 20 /
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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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