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- PDB-2gc1: The crystal structure of phosphoglucose isomerase from Pyrococcus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gc1 | ||||||
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Title | The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with sorbitol 6-phosphate and zinc | ||||||
![]() | Glucose-6-phosphate isomerase | ||||||
![]() | ISOMERASE / cupin / phosphoglucose isomerase / sorbitol 6-phosphate | ||||||
Function / homology | ![]() glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Berrisford, J.M. / Rice, D.W. / Baker, P.J. | ||||||
![]() | ![]() Title: Evidence Supporting a cis-enediol-based Mechanism for Pyrococcus furiosus Phosphoglucose Isomerase Authors: Berrisford, J.M. / Hounslow, A.M. / Akerboom, J. / Hagen, W.R. / Brouns, S.J. / van der Oost, J. / Murray, I.A. / Michael Blackburn, G. / Waltho, J.P. / Rice, D.W. / Baker, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
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PDB format | ![]() | 72 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gc0C ![]() 2gc2C ![]() 2gc3C ![]() 1x8eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21378.273 Da / Num. of mol.: 2 / Fragment: phosphoglucose isomerase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.05 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 20% PEG monoethyl ether 2000, 5 mM D-sorbitol 6-phosphate, 5mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2005 / Details: Osmic Varimax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→69.673 Å / Num. all: 28380 / Num. obs: 28380 / % possible obs: 92.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.95→2.06 Å / % possible obs: 88.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2 / Num. measured all: 17653 / Num. unique obs: 3961 / Rsym value: 0.379 / % possible all: 88.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X8E Resolution: 1.95→19.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.163 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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