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Yorodumi- PDB-2f3m: Structure of human GLUTATHIONE S-TRANSFERASE M1A-1A complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f3m | ||||||
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Title | Structure of human GLUTATHIONE S-TRANSFERASE M1A-1A complexed with 1-(S-(GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXADIENATE ANION | ||||||
Components | Glutathione S-transferase Mu 1 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER / ACTIVE SITE / TRANSITION STATE ANALOGUE | ||||||
Function / homology | Function and homology information nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / hepoxilin biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / hepoxilin biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / glutathione metabolic process / enzyme binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Patskovsky, Y. / Patskovska, L. / Almo, S.C. / Listowsky, I. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Transition state model and mechanism of nucleophilic aromatic substitution reactions catalyzed by human glutathione S-transferase M1a-1a. Authors: Patskovsky, Y. / Patskovska, L. / Almo, S.C. / Listowsky, I. #1: Journal: Biochemistry / Year: 1999 Title: Function of His107 in the Catalytic Mechanism of Human Glutathione S-Transferase Hgstm1A-1A Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f3m.cif.gz | 275.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f3m.ent.gz | 224.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/2f3m ftp://data.pdbj.org/pub/pdb/validation_reports/f3/2f3m | HTTPS FTP |
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-Related structure data
Related structure data | 1xw6C 1xwkC 1gtuS 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 217 / Label seq-ID: 2 - 218
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Details | The biological assembly is a homodimer composed of two identical monomers. The unit cell/asymmetric unit contains 3 full homodimers |
-Components
#1: Protein | Mass: 25746.842 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM1, GST1 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09488, glutathione transferase #2: Chemical | ChemComp-GTD / #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: 2.35 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 280 K / pH: 6 Details: 20% PEG 4000, pH 6.00, VAPOR DIFFUSION, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 11, 2005 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.667→100 Å / Num. obs: 38744 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Rsym value: 0.042 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.67→2.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.32 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GTU Resolution: 2.7→20 Å / SU B: 20.024 / SU ML: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1789 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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