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- PDB-6ynd: GAPDH purified from the supernatant of HEK293F cells: crystal for... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ynd | |||||||||
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Title | GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4. | |||||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
![]() | BIOSYNTHETIC PROTEIN / HEK293F / kifunensine / Cysteine-S-Sulfonic acid | |||||||||
Function / homology | ![]() peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / nuclear membrane / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / vesicle / killing of cells of another organism / protein stabilization / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Roversi, P. / Lia, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Authors: Lia, A. / Dowle, A. / Taylor, C. / Santino, A. / Roversi, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 989.9 KB | Display | ![]() |
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PDB format | ![]() | 835.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yneC ![]() 6ynfC ![]() 6ynhC ![]() 1u8fS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36179.230 Da / Num. of mol.: 8 / Mutation: C152X / Source method: isolated from a natural source Details: GAPDH with catalytic Cys partially oxidised to Cys-S-Sulfonic Acid Source: (natural) ![]() References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups #2: Chemical | ChemComp-XPE / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % / Description: Prism |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% ...Details: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2019 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→140.09 Å / Num. obs: 295271 / % possible obs: 69.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.52→1.71 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14763 / CC1/2: 0.608 / Rpim(I) all: 0.444 / Rrim(I) all: 1.161 / % possible all: 12.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U8F Resolution: 1.525→140.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.095 Details: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including ...Details: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ratio mixture of Cys and Cys S-Sulfonic acid was initially modelled in Fo-Fc residual density. At each Cys152 site, occupancies for Cys and Cys S-Sulfonic acid were refined and constrained so that they sum up to 1.000 plus or minus 0.005.
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Displacement parameters | Biso mean: 27.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.525→140.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.525→1.63 Å
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