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Yorodumi- PDB-6g7d: Structure of MeT1 from Mycobacterium hassiacum in complex with SA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g7d | ||||||
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Title | Structure of MeT1 from Mycobacterium hassiacum in complex with SAM and glycerol. | ||||||
Components | Methyltransferase domain protein | ||||||
Keywords | TRANSFERASE / 3-O-methyltransferase | ||||||
Function / homology | Function and homology information MMP 1-O-methyltransferase / chondroitin sulfate biosynthetic process / DIM/DIP cell wall layer assembly / methyltransferase activity / methylation / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium hassiacum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Pereira, P.J.B. / Ripoll-Rozada, J. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides. Authors: Ripoll-Rozada, J. / Costa, M. / Manso, J.A. / Maranha, A. / Miranda, V. / Sequeira, A. / Ventura, M.R. / Macedo-Ribeiro, S. / Pereira, P.J.B. / Empadinhas, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g7d.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g7d.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 6g7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/6g7d ftp://data.pdbj.org/pub/pdb/validation_reports/g7/6g7d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25445.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria) Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: C731_4163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5B7F3 |
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-Non-polymers , 5 types, 291 molecules
#2: Chemical | ChemComp-SAH / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl pH 8.5, 0.2 M Magnesium chloride, 20% (wt/vol) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→49.222 Å / Num. obs: 67165 / % possible obs: 100 % / Redundancy: 18.5 % / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Mean I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.222 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→49.222 Å
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Refine LS restraints |
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LS refinement shell |
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