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Yorodumi- PDB-1nbi: Structure of R175K mutated glycine N-methyltransferase complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nbi | ||||||
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Title | Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM. | ||||||
Components | Glycine N-methyltransferase | ||||||
Keywords | TRANSFERASE / Methyltransferase / Glycine N-methyltransferase / Catalytic mechanism / Dynamical catalysis | ||||||
Function / homology | Function and homology information 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 / regulation of gluconeogenesis / glycine binding / glycogen metabolic process / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Takata, Y. / Takusagawa, F. | ||||||
Citation | Journal: Biochemistry / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nbi.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nbi.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nbi_validation.pdf.gz | 586.4 KB | Display | wwPDB validaton report |
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Full document | 1nbi_full_validation.pdf.gz | 644.2 KB | Display | |
Data in XML | 1nbi_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 1nbi_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nbi ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nbi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32432.818 Da / Num. of mol.: 4 / Mutation: R175K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GNMT / Organ: liver / Production host: Escherichia coli (E. coli) / References: UniProt: P13255, glycine N-methyltransferase #2: Chemical | ChemComp-SAM / #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: 2.65 Å3/Da / Density % sol: 53.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 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: 3→10 Å / Num. obs: 25997 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3→3.1 Å / % possible all: 85 |
Reflection | *PLUS Num. obs: 25540 / % possible obs: 98 % / Num. measured all: 145578 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.266 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→10 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.29 / Rfactor Rwork: 0.172 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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