+Open data
-Basic information
Entry | Database: PDB / ID: 1u0e | ||||||
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Title | Crystal structure of mouse phosphoglucose isomerase | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / aldose-ketose isomerase / dimer | ||||||
Function / homology | Function and homology information glycolytic process through glucose-6-phosphate / Glycolysis / Gluconeogenesis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / canonical glycolysis ...glycolytic process through glucose-6-phosphate / Glycolysis / Gluconeogenesis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / Neutrophil degranulation / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / glycolytic process / growth factor activity / response to estradiol / myelin sheath / glucose homeostasis / in utero embryonic development / negative regulation of neuron apoptotic process / learning or memory / ubiquitin protein ligase binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Solomons, J.T.G. / Zimmerly, E.M. / Burns, S. / Krishnamurthy, N. / Swan, M.K. / Krings, S. / Muirhead, H. / Chirgwin, J. / Davies, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The crystal structure of mouse phosphoglucose isomerase at 1.6A resolution and its complex with glucose 6-phosphate reveals the catalytic mechanism of sugar ring opening. Authors: Graham Solomons, J.T. / Zimmerly, E.M. / Burns, S. / Krishnamurthy, N. / Swan, M.K. / Krings, S. / Muirhead, H. / Chirgwin, J. / Davies, C. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUE 263 IS A LEU NOT A PHE AS SHOWN BY THE SEQUENCE OF THE CONSTRUCT AS WELL AS THE ...SEQUENCE RESIDUE 263 IS A LEU NOT A PHE AS SHOWN BY THE SEQUENCE OF THE CONSTRUCT AS WELL AS THE ELECTRON DENSITY MAP. IT APPEARS TO EMANATE FROM THE ORIGINAL EXPRESSED SEQUENCE TAG AND IS NOT A PCR ERROR. HENCE THIS IS A POLYMORPHISM IN THE MAMMARY CELL LINE USED TO MAKE THE CDNA. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0e.cif.gz | 252.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0e.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 1u0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0e ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0e | HTTPS FTP |
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-Related structure data
Related structure data | 1u0fC 1u0gC 1n8tS 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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Details | The biological unit is a dimer. The asymmetric unit is a dimer |
-Components
#1: Protein | Mass: 63644.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpi / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3pLysS / References: UniProt: P06745, glucose-6-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-GOL / #5: 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: 2.3 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.9 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2001 / Details: mirrors |
Radiation | Monochromator: Osmic mirros / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.7 Å / Num. all: 148767 / Num. obs: 147857 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.5 / Num. unique all: 14817 / Rsym value: 0.422 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N8T Resolution: 1.6→14.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.67 / SU ML: 0.086 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.439 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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