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Yorodumi- PDB-1f3b: CRYSTAL STRUCTURE OF MGSTA1-1 IN COMPLEX WITH GLUTATHIONE CONJUGA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f3b | ||||||
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Title | CRYSTAL STRUCTURE OF MGSTA1-1 IN COMPLEX WITH GLUTATHIONE CONJUGATE OF BENZO[A]PYRENE EPOXIDE | ||||||
Components | GLUTATHIONE S-TRANSFERASE YA CHAIN | ||||||
Keywords | TRANSFERASE / glutathione S-transferase / GST / BPDE | ||||||
Function / homology | Function and homology information Heme degradation / Azathioprine ADME / Glutathione conjugation / response to stilbenoid / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / dinitrosyl-iron complex binding / glutathione derivative biosynthetic process / glutathione binding / steroid delta-isomerase activity / prostaglandin metabolic process ...Heme degradation / Azathioprine ADME / Glutathione conjugation / response to stilbenoid / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / dinitrosyl-iron complex binding / glutathione derivative biosynthetic process / glutathione binding / steroid delta-isomerase activity / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / xenobiotic metabolic process / response to bacterium / peroxidase activity / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Gu, Y. / Singh, S.V. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Residue R216 and catalytic efficiency of a murine class alpha glutathione S-transferase toward benzo[a]pyrene 7(R),8(S)-diol 9(S), 10(R)-epoxide. Authors: Gu, Y. / Singh, S.V. / Ji, X. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f3b.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f3b.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f3b ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f3b | HTTPS FTP |
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-Related 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: 25530.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET-11D / Production host: Escherichia coli (E. coli) / References: UniProt: P13745, glutathione transferase #2: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.21 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0087 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0087 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 31785 / Num. obs: 31332 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.15 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.05 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.48 / Num. unique all: 3078 / % possible all: 97.5 |
Reflection shell | *PLUS % possible obs: 97.5 % / Mean I/σ(I) obs: 2.42 |
-Processing
Software |
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Refinement | Resolution: 2→40 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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