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- PDB-1q8j: Cobalamin-dependent methionine synthase (1-566) from Thermotoga m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q8j | ||||||
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Title | Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+, Hcy, methyltetrahydrofolate complex) | ||||||
![]() | 5-methyltetrahydrofolate S-homocysteine methyltransferase | ||||||
![]() | TRANSFERASE / homocysteine / methionine / folate / cobalamin / vitamin b12 | ||||||
Function / homology | ![]() methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evans, J.C. / Huddler, D.P. / Hilgers, M.T. / Romanchuk, G. / Matthews, R.G. / Ludwig, M.L. | ||||||
![]() | ![]() Title: Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase. Authors: Evans, J.C. / Huddler, D.P. / Hilgers, M.T. / Romanchuk, G. / 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 | ![]() | 231.7 KB | Display | ![]() |
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PDB format | ![]() | 185.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 950.5 KB | Display | ![]() |
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Full document | ![]() | 974.9 KB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 63.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 63633.148 Da / Num. of mol.: 2 / Fragment: MetH_Tm (residues 1-566) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: propylene glycol, glycerol, PEG 8000, citrate, 1,2,3-heptanetriol, cadmium, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 99097 / Num. obs: 97473 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.99 Å / % possible all: 99.1 |
Reflection | *PLUS % possible obs: 92.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 85.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.06 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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