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Yorodumi- PDB-6h40: High resolution structure of MeT1 from Mycobacterium hassiacum in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h40 | ||||||
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Title | High resolution structure of MeT1 from Mycobacterium hassiacum in complex with 3-methoxy-1,2-propanediol. | ||||||
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 | Mycolicibacterium hassiacum DSM 44199 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.053 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 | 6h40.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h40.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 6h40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h40_validation.pdf.gz | 729.2 KB | Display | wwPDB validaton report |
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Full document | 6h40_full_validation.pdf.gz | 729.2 KB | Display | |
Data in XML | 6h40_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6h40_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/6h40 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/6h40 | HTTPS FTP |
-Related structure data
Related structure data | 6g7dSC 6g80C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-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.) Mycolicibacterium hassiacum DSM 44199 (bacteria) Gene: C731_4163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5B7F3 |
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-Non-polymers , 6 types, 289 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FW5 / ( | #4: Chemical | ChemComp-SAH / | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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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: 2.98 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 293 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: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979295 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979295 Å / Relative weight: 1 |
Reflection | Resolution: 1.053→97.977 Å / Num. obs: 138507 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.053→1.071 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G7D Resolution: 1.053→48.988 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.053→48.988 Å
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Refine LS restraints |
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LS refinement shell |
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