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Yorodumi- PDB-5ueh: Structure of GSTO1 covalently conjugated to quinolinic acid fluor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ueh | ||||||
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Title | Structure of GSTO1 covalently conjugated to quinolinic acid fluorosulfate | ||||||
Components | Glutathione S-transferase omega-1 | ||||||
Keywords | TRANSFERASE/OXIDOREDUCTASE / arylfluorosulfate / GST / covalent inhibitor / TRANSFERASE-OXIDOREDUCTASE complex | ||||||
Function / homology | Function and homology information positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / oxidoreductase activity / extracellular exosome / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mortenson, D.E. / Wilson, I.A. / Kelly, J.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: "Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates. Authors: Mortenson, D.E. / Brighty, G.J. / Plate, L. / Bare, G. / Chen, W. / Li, S. / Wang, H. / Cravatt, B.F. / Forli, S. / Powers, E.T. / Sharpless, K.B. / Wilson, I.A. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ueh.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ueh.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ueh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/5ueh ftp://data.pdbj.org/pub/pdb/validation_reports/ue/5ueh | HTTPS FTP |
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-Related structure data
Related structure data | 5ui4C 4is0S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27686.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Production host: Escherichia coli (E. coli) References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase | ||||
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#2: Chemical | ChemComp-85P / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: 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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 5 mg/mL solution of protein crystallized from precipitant solution containing 2.4 M ammonium sulfate and 0.1 M MES solution pH 5. Crystals cryoprotected by brief immersion in solution ...Details: 5 mg/mL solution of protein crystallized from precipitant solution containing 2.4 M ammonium sulfate and 0.1 M MES solution pH 5. Crystals cryoprotected by brief immersion in solution containing 1.5 M ammonium sulfate, 25% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 9, 2016 / Details: Osmic VariMax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.5 Å / Num. obs: 18695 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.043 / Rsym value: 0.118 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2695 / CC1/2: 0.704 / Rpim(I) all: 0.329 / Rsym value: 0.914 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4IS0 Resolution: 2→49.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.214 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.165 / 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: 33.638 Å2
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Refinement step | Cycle: 1 / Resolution: 2→49.5 Å
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