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Yorodumi- PDB-1usb: Rational design of a novel enzyme - efficient thioester hydrolysi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1usb | ||||||
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Title | Rational design of a novel enzyme - efficient thioester hydrolysis enabled by the incorporation of a single His residue into human glutathione transferase A1-1 | ||||||
Components | GLUTATHIONE S-TRANSFERASE A1 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE | ||||||
Function / homology | Function and homology information Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / epithelial cell differentiation / xenobiotic metabolic process / glutathione metabolic process / fatty acid binding / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å | ||||||
Authors | Jakobsson, E. / Kleywegt, G.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Incorporation of a Single His Residue by Rational Design Enables Thiol-Ester Hydrolysis by Human Glutathione Transferase A1-1 Authors: Hederos, S. / Broo, K.S. / Jakobsson, E. / Kleywegt, G.J. / Mannervik, B. / Baltzer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1usb.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1usb.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 1usb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1usb_validation.pdf.gz | 908.2 KB | Display | wwPDB validaton report |
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Full document | 1usb_full_validation.pdf.gz | 914.4 KB | Display | |
Data in XML | 1usb_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1usb_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/1usb ftp://data.pdbj.org/pub/pdb/validation_reports/us/1usb | HTTPS FTP |
-Related structure data
Related structure data | 1gsdS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25922.307 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-21A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.3 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M TRISHCL PH 7.8, 26 % PEG4000, 2 MM DITHIOTHREITOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.007 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2003 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→67.42 Å / Num. obs: 28011 / % possible obs: 99 % / Redundancy: 5.02 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.6541 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.43 / % possible all: 93.4 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1GSD Resolution: 2.07→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.311 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE LAST REFINEMENT ROUND WAS DONE AGAINST ALL DATA, RFREE VALUES ARE THE LAST RECORDED. THE OCCUPANCY HAS BEEN SET TO 0 WHERE THERE IS NO DENSITY FOR THE SIDE CHAIN.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→40 Å
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Refine LS restraints |
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