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Yorodumi- PDB-1md4: A folding mutant of human class pi glutathione transferase, creat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1md4 | ||||||
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Title | A folding mutant of human class pi glutathione transferase, created by mutating glycine 146 of the wild-type protein to valine | ||||||
Components | pi glutathione transferase | ||||||
Keywords | TRANSFERASE / GST / nucleation mechanism / conserved folding module | ||||||
Function / homology | Function and homology information S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / glutathione derivative biosynthetic process / hepoxilin biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / glutathione derivative biosynthetic process / hepoxilin biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of MAPK cascade / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / xenobiotic metabolic process / glutathione metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / fatty acid binding / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kong, G.K.-W. / Dragani, B. / Aceto, A. / Cocco, R. / Mannervik, B. / Stenberg, G. / McKinstry, W.J. / Polekhina, G. / Parker, M.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Contribution of Glycine 146 to a Conserved Folding Module Affecting Stability and Refolding of Human Glutathione Transferase P1-1 Authors: Kong, G.K.-W. / Polekhina, G. / McKinstry, W.J. / Parker, M.W. / Dragani, B. / Aceto, A. / Paludi, D. / Principe, D.R. / Mannervik, B. / Stenberg, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1md4.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1md4.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 1md4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1md4_validation.pdf.gz | 721.5 KB | Display | wwPDB validaton report |
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Full document | 1md4_full_validation.pdf.gz | 728.3 KB | Display | |
Data in XML | 1md4_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1md4_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1md4 ftp://data.pdbj.org/pub/pdb/validation_reports/md/1md4 | HTTPS FTP |
-Related structure data
Related structure data | 1md3C 10gsS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 23288.650 Da / Num. of mol.: 2 / Mutation: G145V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pKHP1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL_1 Blue / References: UniProt: P09211, glutathione transferase #2: Chemical | #3: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: MES, PEG 8000, calcium chloride, DTT(dithiothreitol), glutathione(reduced), pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 3, 2001 / Details: Mirrors |
Radiation | Monochromator: nickel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. all: 27057 / Num. obs: 25365 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.9 / % possible all: 79.3 |
Reflection | *PLUS Num. measured all: 78780 |
Reflection shell | *PLUS % possible obs: 79.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 10GS Resolution: 2.1→14.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1689082.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.5387 Å2 / ksol: 0.358244 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→14.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.17 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 24085 / Rfactor Rfree: 0.236 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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