+Open data
-Basic information
Entry | Database: PDB / ID: 1msk | ||||||
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Title | METHIONINE SYNTHASE (ACTIVATION DOMAIN) | ||||||
Components | COBALAMIN-DEPENDENT METHIONINE SYNTHASE | ||||||
Keywords | METHYLTRANSFERASE / TRANSFERASE / METHIONINE BIOSYNTHESIS / VITAMIN B12 | ||||||
Function / homology | Function and homology information methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methylation / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.8 Å | ||||||
Authors | Dixon, M.M. / Huang, S. / Matthews, R.G. / Ludwig, M.L. | ||||||
Citation | Journal: Structure / Year: 1996 Title: The structure of the C-terminal domain of methionine synthase: presenting S-adenosylmethionine for reductive methylation of B12. Authors: Dixon, M.M. / Huang, S. / Matthews, R.G. / Ludwig, M. #1: Journal: Science / Year: 1994 Title: How a Protein Binds B12: A 3.0 A X-Ray Structure of B12-Binding Domains of Methionine Synthase Authors: Drennan, C.L. / Huang, S. / Drummond, J.T. / Matthews, R.G. / Ludwig, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1msk.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1msk.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 1msk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1msk ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1msk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37749.168 Da / Num. of mol.: 1 / Fragment: ACTIVATION DOMAIN, RESIDUES 897 - 1227 / Source method: isolated from a natural source Details: GENERATED BY TRYPSIN CLEAVAGE OF THE METHIONINE SYNTHASE HOLOENZYME Source: (natural) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12, DH5AF'-P4B6.3 / References: UniProt: P13009, methionine synthase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-SAM / |
#4: Water | ChemComp-HOH / |
Compound details | THE ACTIVATION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: ADSC / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 28762 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.0532 / Net I/σ(I): 10.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→10 Å / σ(F): 0 Details: TWO LOOPS, CONSISTING OF RESIDUES 965 - 967 AND 1035 - 1036, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > 50.0 A**2. THREE RESIDUES AT THE C-TERMINAL END, 1225 - 1227, ARE DISORDERED, ...Details: TWO LOOPS, CONSISTING OF RESIDUES 965 - 967 AND 1035 - 1036, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > 50.0 A**2. THREE RESIDUES AT THE C-TERMINAL END, 1225 - 1227, ARE DISORDERED, WITH AVERAGE MAIN-CHAIN B-FACTORS > 50.0 A**2.
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Displacement parameters | Biso mean: 21.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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