+Open data
-Basic information
Entry | Database: PDB / ID: 1jlh | ||||||
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Title | Human Glucose-6-phosphate Isomerase | ||||||
Components | phosphoglucose isomerase | ||||||
Keywords | ISOMERASE / glycolysis / glyconeogenesis | ||||||
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 / glucose homeostasis / response to estradiol / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / learning or memory / carbohydrate metabolic process / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cordeiro, A.T. | ||||||
Citation | Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2003 Title: Crystal structure of human phosphoglucose isomerase and analysis of the initial catalytic steps Authors: Cordeiro, A.T. / Godoi, P.H.C. / Silva, C.H.T.P. / Garratt, R.C. / Oliva, G. / Thiemann, O.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jlh.cif.gz | 462 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jlh.ent.gz | 379 KB | Display | PDB format |
PDBx/mmJSON format | 1jlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jlh_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 1jlh_full_validation.pdf.gz | 517.1 KB | Display | |
Data in XML | 1jlh_validation.xml.gz | 94 KB | Display | |
Data in CIF | 1jlh_validation.cif.gz | 133.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jlh ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jlh | HTTPS FTP |
-Related structure data
Related structure data | 1dqrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63229.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET29-a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06744, glucose-6-phosphate isomerase #2: 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: 2.41 Å3/Da / Density % sol: 48.64 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 10000, 0.1M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: Cordeiro, A.T., (2001) Acta Crystallogr., D57, 592. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.545 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.545 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→22.21 Å / Num. all: 138847 / Num. obs: 138362 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 15.5 Å2 / Limit h max: 38 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 129 / Limit l min: 0 / Observed criterion F max: 3704005.62 / Observed criterion F min: 24.9 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.1→2.23 Å / Rmerge(I) obs: 0.399 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 2.1 Å / % possible obs: 99.7 % / Num. measured all: 672976 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DQR Resolution: 2.1→22.21 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 53.15 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.4 Å2 / Biso mean: 26.8 Å2 / Biso min: 9.28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→22.21 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Rfactor Rfree: 0.24 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å |