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- PDB-6sjp: Methyltransferase of the MtgA N227A mutant from Desulfitobacteriu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sjp | ||||||
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Title | Methyltransferase of the MtgA N227A mutant from Desulfitobacterium hafniense | ||||||
![]() | Tetrahydromethanopterin S-methyltransferase | ||||||
![]() | TRANSFERASE / Anaerobic Bacteria / Glycine Betaine Metabolism / Methyl Transfer / Cobalamin / Tetrahydrofolate | ||||||
Function / homology | Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / tetrahydromethanopterin S-methyltransferase activity / tetrahydromethanopterin S-methyltransferase / Dihydropteroate synthase-like / one-carbon metabolic process / methylation / Tetrahydromethanopterin S-methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Badmann, T. / Groll, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures in Tetrahydrofolate Methylation in Desulfitobacterial Glycine Betaine Metabolism at Atomic Resolution. Authors: Badmann, T. / Groll, 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 | ![]() | 243.5 KB | Display | ![]() |
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PDB format | ![]() | 197.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sj8SC ![]() 6sjkC ![]() 6sjnC ![]() 6sjoC ![]() 6sjrC ![]() 6sjsC ![]() 6sk4C 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: 33465.246 Da / Num. of mol.: 2 / Mutation: N227A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Dhaf_4327 / Plasmid: pET-28b(+) / Production host: ![]() ![]() References: UniProt: B8FUR2, tetrahydromethanopterin S-methyltransferase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, 27% PEG 3350 |
-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 7, 2019 |
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→30 Å / Num. obs: 43506 / % possible obs: 98.1 % / Redundancy: 4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / Num. unique obs: 6166 / CC1/2: 0.889 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SJ8 Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.85 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.149 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.15 Å2 / Biso mean: 23.403 Å2 / Biso min: 13.54 Å2
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Refinement step | Cycle: final / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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