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Yorodumi- PDB-4wni: Crystal structure of the T229K mutant of human GAPDH at 2.3 angst... -
+Open data
-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 | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / glycolytic / Rossman fold / NAD cofactor / mutant | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex ...Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor 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 / microtubule cytoskeleton organization / cellular response to type II interferon / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / killing of cells of another organism / vesicle / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Garcin, E.D. / White, M.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wni.cif.gz | 743.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wni.ent.gz | 624.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/4wni ftp://data.pdbj.org/pub/pdb/validation_reports/wn/4wni | HTTPS FTP |
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-Related structure data
Related structure data | 4wncC 1u8fS 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: 36127.242 Da / Num. of mol.: 4 / Mutation: T229K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 / Variant: T229K / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRIPL 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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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