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Yorodumi- PDB-6quq: Crystal structure of glutathionylated glycolytic glyceraldehyde-3... -
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-Basic information
Entry | Database: PDB / ID: 6quq | ||||||
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Title | Crystal structure of glutathionylated glycolytic glyceraldehyde-3- phosphate dehydrogenase from Arabidopsis thaliana (AtGAPC1) | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | ||||||
Keywords | OXIDOREDUCTASE / Rossman fold / oxidoreductase activity / NAD / cytosolic / glutathione | ||||||
Function / homology | Function and homology information fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / salicylic acid binding / seed development / response to sucrose / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / apoplast / plant-type vacuole / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope ...fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / salicylic acid binding / seed development / response to sucrose / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / apoplast / plant-type vacuole / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope / response to redox state / chloroplast / gluconeogenesis / glycolytic process / response to hydrogen peroxide / NAD binding / NADP binding / response to heat / response to oxidative stress / copper ion binding / positive regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.993 Å | ||||||
Authors | Fermani, S. / Zaffagnini, M. / Falini, G. / Trost, P. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates. Authors: Zaffagnini, M. / Marchand, C.H. / Malferrari, M. / Murail, S. / Bonacchi, S. / Genovese, D. / Montalti, M. / Venturoli, G. / Falini, G. / Baaden, M. / Lemaire, S.D. / Fermani, S. / Trost, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6quq.cif.gz | 268 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6quq.ent.gz | 221.5 KB | Display | PDB format |
PDBx/mmJSON format | 6quq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/6quq ftp://data.pdbj.org/pub/pdb/validation_reports/qu/6quq | HTTPS FTP |
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-Related structure data
Related structure data | 6qunC 4z0hS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36517.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: glutathynilated enzyme / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPC1, GAPC, GAPDH, At3g04120, T6K12.26 / Organ: cytoplasm / Cell line (production host): BL21DE3 / Production host: Escherichia coli (E. coli) References: UniProt: P25858, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.41 Å3/Da / Density % sol: 48.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.0 M (NH4)2SO4, 0.1 M Hepes-NaOH, 0.1 mM H2O2 and 1 mM GSH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.26 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2012 Details: Cilindrical Mirror with 50 nm Pt-coating, Toridal Mirros with 50 nm Pt-coating |
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.26 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→47.66 Å / Num. obs: 15692 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 18.7 % / Biso Wilson estimate: 69 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.021 / Rrim(I) all: 0.091 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.99→3.16 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 2155 / Rpim(I) all: 0.07 / Rrim(I) all: 0.311 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z0H Resolution: 2.993→47.657 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 27.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.993→47.657 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 38.0316 Å / Origin y: 36.757 Å / Origin z: 236.0123 Å
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Refinement TLS group | Selection details: all |