+Open data
-Basic information
Entry | Database: PDB / ID: 1bhj | ||||||
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Title | CRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT) | ||||||
Components | GLYCINE N-METHYLTRANSFERASE | ||||||
Keywords | METHYLTRANSFERASE / FOLATE BINDING PROTEIN | ||||||
Function / homology | Function and homology information selenol Se-methyltransferase activity / Glyoxylate metabolism and glycine degradation / glycine N-methyltransferase / sarcosine metabolic process / glycine N-methyltransferase activity / 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 / sarcosine metabolic process / glycine N-methyltransferase activity / 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 / glycine binding / regulation of gluconeogenesis / 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 / RIGID BODY REFINEMENT / Resolution: 2.5 Å | ||||||
Authors | Pattanayek, R. / Newcomer, M.E. / Wagner, C. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structure of apo-glycine N-methyltransferase (GNMT). Authors: Pattanayek, R. / Newcomer, M.E. / Wagner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bhj.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bhj.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 1bhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/1bhj ftp://data.pdbj.org/pub/pdb/validation_reports/bh/1bhj | HTTPS FTP |
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-Related structure data
Related structure data | 1xvaS S: Starting model for refinement |
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Similar 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: 32460.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: APO FORM / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13255, glycine N-methyltransferase #2: 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: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 / Details: pH 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 11 ℃ / Method: vapor diffusion, hanging dropDetails: equal volume of protein and reservoir solution were used for the drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 22481 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.106 / Net I/σ(I): 10.59 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.73 / Rsym value: 0.417 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 254910 / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.417 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1XVA Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 33.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.221 |