+Open data
-Basic information
Entry | Database: PDB / ID: 7nc8 | ||||||
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Title | Glutathione-S-transferase GliG mutant S24A | ||||||
Components | Glutathione S-transferase GliG | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Aspergillus fumigatus / mycotoxin / glutathione-S-transferase / carbon-sulphur-bond / epidithiodioxopiperazine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Groll, M. / Huber, E.M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structural and Mechanistic Insights into C-S Bond Formation in Gliotoxin. Authors: Scherlach, K. / Kuttenlochner, W. / Scharf, D.H. / Brakhage, A.A. / Hertweck, C. / 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 | 7nc8.cif.gz | 590.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nc8.ent.gz | 491.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nc8_validation.pdf.gz | 482.6 KB | Display | wwPDB validaton report |
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Full document | 7nc8_full_validation.pdf.gz | 492.7 KB | Display | |
Data in XML | 7nc8_validation.xml.gz | 52 KB | Display | |
Data in CIF | 7nc8_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/7nc8 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/7nc8 | HTTPS FTP |
-Related structure data
Related structure data | 7nc1C 7nc2C 7nc3SC 7nc5C 7nc6C 7nc9C 7ncbC 7ncdC 7nceC 7nclC 7ncmC 7ncnC 7ncoC 7ncpC 7nctC 7ncuC 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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Unit cell |
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-Components
#1: Protein | Mass: 28947.014 Da / Num. of mol.: 6 / Mutation: S24A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold) Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUB_075740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0Y813 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5.5, 25 % PEG3350 |
-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: Nov 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49 Å / Num. obs: 89697 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 11149 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NC3 Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.073 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.79 Å2 / Biso mean: 51.679 Å2 / Biso min: 26.78 Å2
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Refinement step | Cycle: final / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 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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