+Open data
-Basic information
Entry | Database: PDB / ID: 1gzd | ||||||
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Title | Crystal structure of pig phosphoglucose isomerase | ||||||
Components | GLUCOSE-6-PHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / ALDOSE-KETOSE ISOMERASE / GLYCOLYTIC ENZYME / CYTOKINE / MULTIFUNCTIONAL PROTEIN / GLUCONEOGENESIS / GLYCOLYSIS | ||||||
Function / homology | Function and homology information Glycolysis / TP53 Regulates Metabolic Genes / Gluconeogenesis / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Neutrophil degranulation / monosaccharide binding / cytokine activity ...Glycolysis / TP53 Regulates Metabolic Genes / Gluconeogenesis / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Neutrophil degranulation / monosaccharide binding / cytokine activity / gluconeogenesis / glycolytic process / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Davies, C. / Muirhead, H. | ||||||
Citation | Journal: Proteins / Year: 2002 Title: Crystal Structure of Phosphoglucose Isomerase from Pig Muscle and its Complex with 5-Phosphoarabinonate Authors: Davies, C. / Muirhead, H. #1: Journal: Philos.Trans.R.Soc.London / Year: 1981 Title: Glucose 6-Phosphate Isomerase Authors: Achari, A. / Marshall, S.E. / Muirhead, H. / Palmieri, R.H. / Noltmann, E.A. #2: Journal: J.Mol.Biol. / Year: 1977 Title: Crystallographic Structure Analysis of Glucose 6-Phosphate Isomerase at 3.5 A Resolution Authors: Shaw, P.J. / Muirhead, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gzd.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzd.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 1gzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gzd_validation.pdf.gz | 381.7 KB | Display | wwPDB validaton report |
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Full document | 1gzd_full_validation.pdf.gz | 396.3 KB | Display | |
Data in XML | 1gzd_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1gzd_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzd ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzd | HTTPS FTP |
-Related 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: 63077.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Tissue: MUSCLE / References: UniProt: P08059, glucose-6-phosphate isomerase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 277 K / pH: 7 Details: THE PROTEIN WAS CONCENTRATED TO 10MG/ML AND CRYSTALLIZED AT 4 DEGRESS CELSIUS FROM 10MM SODIUM PHOSPHATE, PH 7.5 AND 57% SATURATED AMMONIUM SULPHATE. |
Crystal grow | *PLUS Method: otherDetails: Campbell, J.W., (1971) Cold Spring Harbor Symp Quant Biol., 36, 165. |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Type: SRS |
Detector | Detector: FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.18→31.3 Å / Num. obs: 28680 / % possible obs: 75.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.073 |
Reflection | *PLUS Highest resolution: 2.19 Å / Lowest resolution: 31 Å |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.876 / SU B: 9.405 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 1.623 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NONE
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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