+Open data
-Basic information
Entry | Database: PDB / ID: 5ld0 | ||||||
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Title | Chimeric GST | ||||||
Components | Glutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1 | ||||||
Keywords | TRANSFERASE / Directed evolution / Glutathione transferase A1-1 / protein stability | ||||||
Function / homology | Function and homology information Azathioprine ADME / Glutathione conjugation / response to stilbenoid / Heme degradation / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / : / dinitrosyl-iron complex binding / glutathione derivative biosynthetic process / glutathione binding / steroid delta-isomerase activity ...Azathioprine ADME / Glutathione conjugation / response to stilbenoid / Heme degradation / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / : / dinitrosyl-iron complex binding / glutathione derivative biosynthetic process / glutathione binding / 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 / xenobiotic catabolic process / epithelial cell differentiation / glutathione metabolic process / xenobiotic metabolic process / fatty acid binding / response to bacterium / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Axarli, A. / Muleta, A.W. / Chronopoulou, E.G. / Papageorgiou, A.C. / Labrou, N.E. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: Directed evolution of glutathione transferases towards a selective glutathione-binding site and improved oxidative stability. Authors: Axarli, I. / Muleta, A.W. / Chronopoulou, E.G. / Papageorgiou, A.C. / Labrou, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ld0.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ld0.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 5ld0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ld0 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ld0 | HTTPS FTP |
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-Related structure data
Related structure data | 5lczC 1pkzS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25780.139 Da / Num. of mol.: 1 Fragment: UNP residues 1-85,UNP residues 86-213,UNP residues 214-222 Source method: isolated from a genetically manipulated source Details: Chimeric protein from gene shuffling of rat and human GSTA1-1 Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Rattus norvegicus (Norway rat) Gene: GSTA1, Gsta2 / Production host: Escherichia coli (E. coli) References: UniProt: P08263, UniProt: P04903, glutathione transferase |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium formate 0.15 M, PEG 4000 15% (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 28561 / % possible obs: 96.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 16.95 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1768 / CC1/2: 0.497 / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PKZ Resolution: 1.6→19.277 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.277 Å
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Refine LS restraints |
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LS refinement shell |
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