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Yorodumi- PDB-1c72: TYR115, GLN165 AND TRP209 CONTRIBUTE TO THE 1,2-EPOXY-3-(P-NITROP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c72 | ||||||
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Title | TYR115, GLN165 AND TRP209 CONTRIBUTE TO THE 1,2-EPOXY-3-(P-NITROPHENOXY)PROPANE CONJUGATING ACTIVITIES OF GLUTATHIONE S-TRANSFERASE CGSTM1-1 | ||||||
Components | PROTEIN (GLUTATHIONE S-TRANSFERASE) | ||||||
Keywords | TRANSFERASE / GLUTATHIONE S-TRANSFERASE / 1 / 2-EPOXY-3-(P-NITROPHENOXY)PROPANE / EPOXIDASE ACTIVITY / STEADY-STATE KINETICS | ||||||
Function / homology | Function and homology information Glutathione conjugation / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / Azathioprine ADME / Paracetamol ADME / glutathione transferase / glutathione transferase activity / lipid metabolic process / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Chern, M.K. / Wu, T.C. / Hsieh, C.H. / Chou, C.C. / Liu, L.F. / Kuan, I.C. / Yeh, Y.H. / Hsiao, C.D. / Tam, M.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Tyr115, gln165 and trp209 contribute to the 1, 2-epoxy-3-(p-nitrophenoxy)propane-conjugating activity of glutathione S-transferase cGSTM1-1. Authors: Chern, M.K. / Wu, T.C. / Hsieh, C.H. / Chou, C.C. / Liu, L.F. / Kuan, I.C. / Yeh, Y.H. / Hsiao, C.D. / Tam, M.F. #1: Journal: J.Mol.Biol. / Year: 1998 Title: The Three-Dimensional Structure of an Avian Class-Mu Glutathione S-Transferase, cGSTM1-1 at 1.94A Resolution Authors: Sun, Y.J. / Kuan, I.C. / Tam, M.F. / Hsiao, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c72.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c72.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c72_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1c72_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1c72_validation.xml.gz | 38 KB | Display | |
Data in CIF | 1c72_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c72 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c72 | HTTPS FTP |
-Related structure data
Related structure data | 1gsuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25779.650 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 1,2-EPOXY-3-(P-NITROPHENOXY)PROPANE / Source: (gene. exp.) Gallus gallus (chicken) / Organ: LIVER / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P20136, glutathione transferase #2: Chemical | ChemComp-EPY / #3: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→31 Å / Num. obs: 25597 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.17 / Rsym value: 0.317 / % possible all: 89.2 |
Reflection | *PLUS % possible obs: 86.6 % / Num. measured all: 66453 / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GSU Resolution: 2.8→31 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 31.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 31 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / Rfactor Rfree: 0.35 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.246 |