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Yorodumi- PDB-1nuh: The crystal structure of human phosphoglucose isomerase complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nuh | ||||||
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Title | The crystal structure of human phosphoglucose isomerase complexed with 5-phosphoarabinonate | ||||||
Components | glucose phosphate isomerase | ||||||
Keywords | ISOMERASE / ALDOSE-KETOSE ISOMERASE / GLYCOLYSIS ENZYME / NEUROTROPHIC GROWTH FACTOR / CYTOKINE | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / cytokine activity / gluconeogenesis / response to progesterone / glycolytic process / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / ficolin-1-rich granule lumen / negative regulation of neuron apoptotic process / carbohydrate metabolic process / learning or memory / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / REFINEMENT / Resolution: 2.51 Å | ||||||
Authors | Davies, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: The structure of human phosphoglucose isomerase complexed with a transition-state analogue. Authors: Davies, C. / Muirhead, H. / Chirgwin, J. #1: Journal: J.Mol.Biol. / Year: 2001 Title: The Crystal Structure of Human Phosphoglucose Isomerase at 1.6 A Resolution: Implications for Catalytic Mechanism, Cytokine Activity and Haemolytic Anaemia Authors: Read, J. / Pearce, J. / Li, X. / Muirhead, H. / Chirgwin, J. / Davies, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nuh.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nuh.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nuh_validation.pdf.gz | 460.1 KB | Display | wwPDB validaton report |
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Full document | 1nuh_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 1nuh_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 1nuh_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/1nuh ftp://data.pdbj.org/pub/pdb/validation_reports/nu/1nuh | HTTPS FTP |
-Related structure data
Related structure data | 1iatS 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 | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. The biologically active state is dimeric. The dimer is produced by applying the following operation: y,x,-z |
-Components
#1: Protein | Mass: 63229.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPI / Plasmid: pET5a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06744, glucose-6-phosphate isomerase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Sugar | ChemComp-PA5 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.1 M ammonium sulphate, 100 mM Tris pH 8.5, 5 mM 5-phosphoarabinonate, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Read, J., (2001) J.Mol.Biol., 309, 447. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→94.4 Å / Num. all: 21797 / Num. obs: 21797 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.51→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2171 / Rsym value: 0.254 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: REFINEMENT Starting model: PDN ENTRY 1IAT Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.31 / SU ML: 0.256 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.815 / ESU R Free: 0.324 / 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: 25.156 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.565 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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