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Yorodumi- PDB-6ynf: GAPDH purified from the supernatant of HEK293F cells: crystal for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ynf | |||||||||
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Title | GAPDH purified from the supernatant of HEK293F cells: crystal form 3 of 4. | |||||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / HEK293F / kifunensine / Cysteine-S-Sulfonic acid | |||||||||
Function / homology | Function and homology information 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å | |||||||||
Authors | Roversi, P. / Lia, A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Wellcome Open Res / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ynf.cif.gz | 944.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ynf.ent.gz | 796.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ynf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ynf_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6ynf_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6ynf_validation.xml.gz | 95.7 KB | Display | |
Data in CIF | 6ynf_validation.cif.gz | 131.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/6ynf ftp://data.pdbj.org/pub/pdb/validation_reports/yn/6ynf | HTTPS FTP |
-Related structure data
Related structure data | 6yndSC 6yneC 6ynhC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36048.031 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / Organ: Kidney / Tissue: Epithelium 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.76 % / Description: Prism |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Condition F4 of MORPHEUS screen. 0.12M monosaccharides solution, 0.1M MORPHEUS Buffer System 3, 30% v/v MORPHEUS Precipitant Mix 1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2019 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→135.18 Å / Num. obs: 59243 / % possible obs: 58.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.83 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.27 / Rrim(I) all: 0.29 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.39→2.74 Å / Redundancy: 7 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2962 / CC1/2: 0.591 / Rrim(I) all: 1.38 / % possible all: 8.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YND Resolution: 2.394→135.18 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.366
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Displacement parameters | Biso mean: 39.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.394→135.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.394→2.62 Å
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