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- PDB-8sse: Methionine synthase, C-terminal fragment, Cobalamin and Reactivat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sse | ||||||
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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 | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 113.1 KB | Display | |
Data in CIF | ![]() | 150 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sscC ![]() 8ssdC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 663 - 1185 / Label seq-ID: 1 - 523
NCS ensembles :
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Components
#1: Protein | Mass: 58605.441 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-B12 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis-Tris Propane, pH 7, 60% v/v Tacismate, pH 7, 5% PEG 300, 10% ethylene glycol, 1.5 mM cyanocobalamin |
-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 16, 2022 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→49.295 Å / Num. obs: 64421 / % possible obs: 98.9 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.121 / Rrim(I) all: 0.228 / Χ2: 0.88 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.15→3.23 Å / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.973 / Num. measured all: 15918 / Num. unique obs: 4542 / CC1/2: 0.583 / Rpim(I) all: 0.609 / Rrim(I) all: 1.152 / Χ2: 0.76 / Net I/σ(I) obs: 1.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3bul Resolution: 3.15→49.295 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.865 / WRfactor Rfree: 0.291 / WRfactor Rwork: 0.231 / SU B: 80.383 / SU ML: 0.593 / Average fsc free: 0.9366 / Average fsc work: 0.9604 / Cross valid method: THROUGHOUT / ESU R Free: 0.63 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: 82.81 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→49.295 Å
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Refine LS restraints |
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