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Yorodumi- PDB-1b48: CRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b48 | ||||||
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Title | CRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-HYDROXYNONENAL IN ONE SUBUNIT AND GSH IN THE OTHER: EVIDENCE OF SIGNALING ACROSS DIMER INTERFACE IN MGSTA4-4 | ||||||
Components | PROTEIN (GLUTATHIONE S-TRANSFERASE) | ||||||
Keywords | TRANSFERASE / GLUTATHIONE S-TRANSFERASE / GST / SUBUNIT COOPERATIVITY | ||||||
Function / homology | Function and homology information organic cyclic compound binding / glutathione transferase / glutathione transferase activity / toxic substance binding / glutathione metabolic process / xenobiotic metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Xiao, B. / Zimniak, P. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Crystal structure of a murine glutathione S-transferase in complex with a glutathione conjugate of 4-hydroxynon-2-enal in one subunit and glutathione in the other: evidence of signaling across the dimer interface. Authors: Xiao, B. / Singh, S.P. / Nanduri, B. / Awasthi, Y.C. / Zimniak, P. / Ji, X. #1: Journal: FEBS Lett. / Year: 1998 Title: Crystal Structure of a Murine Alpha-Class Glutathione S-Transferase Involved in Cellular Defense Against Oxidative Stress Authors: Krengel, U. / Schroter, K.H. / Hoier, H. / Arkema, A. / Kalk, K.H. / Zimniak, P. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b48.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b48.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 1b48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b48 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b48 | HTTPS FTP |
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-Related structure data
Related structure data | 1guhS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99956, -0.016641, -0.024543), Vector: |
-Components
#1: Protein | Mass: 25476.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: CYTOPLASM / Organ: LUNG / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / Variant (production host): PET9A/MGSTA4 / References: UniProt: P24472, glutathione transferase #2: Chemical | ChemComp-HAG / | #3: Chemical | ChemComp-GSH / | #4: 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: 2.35 Å3/Da / Density % sol: 47.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 0.11 MM PROTEIN IN 0.047 M HEPES BUFFER (PH 7.5) CONTAINING 1.82 MM GLUTATHIONE, 10.91 MM HNA-SG (GSH CONJUGATE OF 4- ...Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 0.11 MM PROTEIN IN 0.047 M HEPES BUFFER (PH 7.5) CONTAINING 1.82 MM GLUTATHIONE, 10.91 MM HNA-SG (GSH CONJUGATE OF 4-HYDROXYNONENAL), 9.1% ETHANOL, 4.5% ISOPROPANOL, AND 6.5% PEG MONOMETHYL ETHER 5K (PH 7.5). THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING 10% ISOPROPANOL AND 12% PEG MONOMETHYL ETHER 5K IN 80 MM HEPES BUFFER (PH 7.5). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18-20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: May 15, 1997 / 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: 2.6→20 Å / Num. obs: 15647 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.35 / % possible all: 60.1 |
Reflection shell | *PLUS % possible obs: 60.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GUH Resolution: 2.6→20 Å / Data cutoff high absF: 20 / Data cutoff low absF: 2.6 / Cross valid method: FREE R / σ(F): 2 / Details: ALL DATA WERE INCLUDED IN MAP CALCULATIONS.
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Displacement parameters | Biso mean: 49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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