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Yorodumi- PDB-6sk4: Methyltransferase MtgA from Desulfitobacterium hafniense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sk4 | ||||||
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Title | Methyltransferase MtgA from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21) | ||||||
Components | Methylcorrinoid:tetrahydrofolate 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 / Dihydropteroate synthase-like / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / one-carbon metabolic process / methylation / Chem-THH / Methylcorrinoid:tetrahydrofolate methyltransferase Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense Y51 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 6sk4.cif.gz | 471.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sk4.ent.gz | 389.7 KB | Display | PDB format |
PDBx/mmJSON format | 6sk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sk4_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6sk4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6sk4_validation.xml.gz | 46 KB | Display | |
Data in CIF | 6sk4_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6sk4 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6sk4 | HTTPS FTP |
-Related structure data
Related structure data | 6sj8SC 6sjkC 6sjnC 6sjoC 6sjpC 6sjrC 6sjsC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33508.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense Y51 (bacteria) Gene: mtgA, DSY3157 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q24SP6, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-THH / #3: Chemical | ChemComp-GOL / | #4: 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: 1.92 Å3/Da / Density % sol: 35.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM TRIS, 28% 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: 1.55→30 Å / Num. obs: 139692 / % possible obs: 97.2 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.55→1.65 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 24053 / CC1/2: 0.823 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SJ8 Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.723 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.109 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: 61.31 Å2 / Biso mean: 21.902 Å2 / Biso min: 13.29 Å2
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Refinement step | Cycle: final / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 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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