+Open data
-Basic information
Entry | Database: PDB / ID: 5egp | |||||||||
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Title | Crystal structure of the S-methyltransferase TmtA | |||||||||
Components | UbiE/COQ5 family methyltransferase, putative | |||||||||
Keywords | TRANSFERASE / bis-thiomethyltransferase / gliotoxin / epipolythiodioxopiperazine / Aspergillus fumigatus | |||||||||
Function / homology | ubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / UbiE/COQ5 family methyltransferase, putative Function and homology information | |||||||||
Biological species | Aspergillus fumigatus Z5 (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | |||||||||
Authors | Duell, E.R. / Glaser, M. / Antes, I. / Groll, M. / Huber, E.M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Sequential Inactivation of Gliotoxin by the S-Methyltransferase TmtA. Authors: Duell, E.R. / Glaser, M. / Le Chapelain, C. / Antes, I. / Groll, M. / Huber, E.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5egp.cif.gz | 254.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5egp.ent.gz | 211.1 KB | Display | PDB format |
PDBx/mmJSON format | 5egp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/5egp ftp://data.pdbj.org/pub/pdb/validation_reports/eg/5egp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 35637.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_02735 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0J5Q3C4*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium acetate, 2.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45 Å / Num. obs: 89458 / % possible obs: 95.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.5→1.6 Å / Rmerge(I) obs: 0.53 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.323 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.689 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→15 Å
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Refine LS restraints |
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