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Yorodumi- PDB-6sjs: Methyltransferase of the MtgA N227A mutant from Desulfitobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sjs | ||||||
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Title | Methyltransferase of the MtgA N227A mutant from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate | ||||||
Components | Tetrahydromethanopterin S-methyltransferase | ||||||
Keywords | 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 / Chem-THH / Tetrahydromethanopterin S-methyltransferase Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense DCB-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Badmann, T. / Groll, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chembiochem / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sjs.cif.gz | 248.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sjs.ent.gz | 200.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sjs_validation.pdf.gz | 971.2 KB | Display | wwPDB validaton report |
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Full document | 6sjs_full_validation.pdf.gz | 973.8 KB | Display | |
Data in XML | 6sjs_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6sjs_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/6sjs ftp://data.pdbj.org/pub/pdb/validation_reports/sj/6sjs | HTTPS FTP |
-Related structure data
Related structure data | 6sj8SC 6sjkC 6sjnC 6sjoC 6sjpC 6sjrC 6sk4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Desulfitobacterium hafniense DCB-2 (bacteria) Gene: Dhaf_4327 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B8FUR2, tetrahydromethanopterin S-methyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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: 1.8→30 Å / Num. obs: 51389 / % possible obs: 98.1 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7642 / CC1/2: 0.726 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SJ8 Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.4 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.128 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: 60.05 Å2 / Biso mean: 22.296 Å2 / Biso min: 9.97 Å2
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Refinement step | Cycle: final / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | T12: 0.0001 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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