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Yorodumi- PDB-2idk: Crystal Structure of Rat Glycine N-Methyltransferase Complexed Wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2idk | ||||||
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Title | Crystal Structure of Rat Glycine N-Methyltransferase Complexed With Folate | ||||||
Components | Glycine N-methyltransferase | ||||||
Keywords | TRANSFERASE / Glycine N-Methyltransferase / rat / folate binding | ||||||
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Egli, M. / Newcomer, M.E. / Wagner, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: 5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding protein glycine N-methyltransferase. Authors: Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Egli, M. / 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 | 2idk.cif.gz | 227.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2idk.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 2idk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/2idk ftp://data.pdbj.org/pub/pdb/validation_reports/id/2idk | HTTPS FTP |
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-Related structure data
Related structure data | 2idjC 1bhjS S: Starting model for refinement C: citing same article (ref.) |
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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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley / Gene: GNMT / Plasmid: pR6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13255, glycine N-methyltransferase #2: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.1 M Ca acetate, 0.025 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2006 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 38846 / Num. obs: 38846 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 56.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3625 / Rsym value: 0.45 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1BHJ Resolution: 2.55→29 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 62 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.029
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