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Open data
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Basic information
Entry | Database: PDB / ID: 1k7y | ||||||
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Title | E. coli MetH C-terminal fragment (649-1227) | ||||||
![]() | methionine synthase | ||||||
![]() | TRANSFERASE / MOTION OF 4-HELIX BUNDLE / DOMAIN INTERACTIONS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bandarian, V. / Pattridge, K.A. / Lennon, B.W. / Huddler, D.P. / Matthews, R.G. / Ludwig, M.L. | ||||||
![]() | ![]() Title: Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. Authors: Bandarian, V. / Pattridge, K.A. / Lennon, B.W. / Huddler, D.P. / Matthews, R.G. / Ludwig, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k98C ![]() 1bmtS ![]() 1mskS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 64859.137 Da / Num. of mol.: 1 / Fragment: c-terminal activation complex, residues 651-1227 / Mutation: H759G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-B12 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.31 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 17, 2000 / Details: Yale mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 18414 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rsym value: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.396 / % possible all: 95.4 |
Reflection | *PLUS Lowest resolution: 27 Å / Num. obs: 18245 / Num. measured all: 80208 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 95.4 % / Rmerge(I) obs: 0.396 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entries 1msk and 1bmt Resolution: 3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.218 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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