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Yorodumi- PDB-1u8f: Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u8f | ||||||
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Title | Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase At 1.75 Resolution | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase, liver | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / ROSSMANN FOLD / DEHYDROGENASE / MAMMALIAN GAPDH / GAPD | ||||||
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: 1.75 Å | ||||||
Authors | Jenkins, J.L. / Tanner, J.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase. Authors: Jenkins, J.L. / Tanner, J.J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: A human nuclear uracil DNA glycosylase is the 37-kDa subunit of glyceraldehyde-3-Phosphate Dehydrogenase Authors: Meyer-Siegler, K. / Mauro, D.J. / Seal, G. / Wurzer, J. / deRiel, J.K. / Sirover, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u8f.cif.gz | 274.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u8f.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 1u8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u8f_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1u8f_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1u8f_validation.xml.gz | 57.7 KB | Display | |
Data in CIF | 1u8f_validation.cif.gz | 83 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/1u8f ftp://data.pdbj.org/pub/pdb/validation_reports/u8/1u8f | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 36099.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Placental / Gene: GAPD / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | #3: 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: 2.25 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | Temperature: 295 K / pH: 7 Details: PEG 3350, SUCCINIC ACID, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 141888 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED STRUCTURE Resolution: 1.75→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3099319.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.28 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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