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- PDB-8ssd: Methionine synthase, C-terminal fragment, Cobalamin and Reactivat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ssd | ||||||
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Title | Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8 | ||||||
![]() | Methionine synthase | ||||||
![]() | TRANSFERASE / Methyl transferase / cobalamin-dependent / methionine synthase / cobalamin binding / one-carbon metabolism | ||||||
Function / homology | ![]() methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, K. / Mendoza, J. / Koutmos, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo. Authors: Mendoza, J. / Purchal, M. / Yamada, K. / Koutmos, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 313.4 KB | Display | ![]() |
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PDB format | ![]() | 252.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8sscC ![]() 8sseC ![]() 3bulS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 58605.441 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium Acetate, pH 4.6, 2 M Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing, with two horizontally deflecting mirrors | ||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→40.55 Å / Num. obs: 76051 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.061 / Rrim(I) all: 0.187 / Χ2: 0.92 / Net I/σ(I): 8.1 / Num. measured all: 711608 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.45 Å / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.903 / Num. measured all: 42258 / Num. unique obs: 4396 / CC1/2: 0.667 / Rpim(I) all: 0.306 / Rrim(I) all: 0.954 / Χ2: 0.92 / Net I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BUL Resolution: 2.4→39.85 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.829 / SU B: 8.23 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.065 Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→39.85 Å
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Refine LS restraints |
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