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- PDB-4wni: Crystal structure of the T229K mutant of human GAPDH at 2.3 angst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wni | ||||||
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Title | Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / glycolytic / Rossman fold / NAD cofactor / mutant | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Garcin, E.D. / White, M.R. | ||||||
![]() | ![]() Title: A Dimer Interface Mutation in Glyceraldehyde-3-Phosphate Dehydrogenase Regulates Its Binding to AU-rich RNA. Authors: White, M.R. / Khan, M.M. / Deredge, D. / Ross, C.R. / Quintyn, R. / Zucconi, B.E. / Wysocki, V.H. / Wintrode, P.L. / Wilson, G.M. / Garcin, E.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 743.6 KB | Display | ![]() |
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PDB format | ![]() | 624.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wncC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 36127.242 Da / Num. of mol.: 4 / Mutation: T229K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG3350, 0.02 M ZnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.5 Å / Num. obs: 63669 / % possible obs: 88.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.6 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 12.1 / % possible all: 55.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U8F Resolution: 2.3→49.5 Å / Cross valid method: FREE R-VALUE / Phase error: 0.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.5 Å
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LS refinement shell | Resolution: 2.3→2.38 Å
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