+Open data
-Basic information
Entry | Database: PDB / ID: 5jgl | ||||||
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Title | Crystal structure of GtmA in complex with S-Adenosylmethionine | ||||||
Components | UbiE/COQ5 family methyltransferase, putative | ||||||
Keywords | TRANSFERASE / Aspergillus fumigatus / Methyltransferase / S-Adenosylmethionine / Gliotoxin / Resistance | ||||||
Function / homology | ubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / UbiE/COQ5 family methyltransferase, putative Function and homology information | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Dolan, S.K. / Bock, T. / Hering, V. / Jones, G.W. / Blankenfeldt, W. / Doyle, S. | ||||||
Citation | Journal: Open Biol / Year: 2017 Title: Structural, mechanistic and functional insight into gliotoxinbis-thiomethylation inAspergillus fumigatus. Authors: Dolan, S.K. / Bock, T. / Hering, V. / Owens, R.A. / Jones, G.W. / Blankenfeldt, W. / Doyle, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jgl.cif.gz | 204.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jgl.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jgl_validation.pdf.gz | 921.5 KB | Display | wwPDB validaton report |
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Full document | 5jgl_full_validation.pdf.gz | 922.9 KB | Display | |
Data in XML | 5jgl_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5jgl_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jgl ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jgl | HTTPS FTP |
-Related 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: 32455.912 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: Y699_02735 / Variant: ATCC 26933 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J5Q3C4 #2: Chemical | #3: Chemical | #4: 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: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M sodium phosphate citrate pH 4.2, 22% (w/v) PEG 8000, 0.08% (w/v) ellipticine, 0.20% (w/v) gibbeellin A3, 0.20% (w/v) trans-cinnamic acid, 0.20% (w/v) phenol, 0.20% (w/v) succinic acid ...Details: 0.1 M sodium phosphate citrate pH 4.2, 22% (w/v) PEG 8000, 0.08% (w/v) ellipticine, 0.20% (w/v) gibbeellin A3, 0.20% (w/v) trans-cinnamic acid, 0.20% (w/v) phenol, 0.20% (w/v) succinic acid disodium salt hexahydrate and 0.02 M HEPES pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.3855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.3855 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.28→49.275 Å / Num. obs: 50076 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 19.5 % / Biso Wilson estimate: 32.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.08 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→49.275 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 26.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 184.69 Å2 / Biso mean: 44.7729 Å2 / Biso min: 18.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.28→49.275 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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