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- PDB-1j3r: Crystal structure of Thermococcus litoralis phosphogrucose isomer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j3r | ||||||
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Title | Crystal structure of Thermococcus litoralis phosphogrucose isomerase complexed with gluconate-6-phosphate | ||||||
![]() | Phosphoglucose Isomerase | ||||||
![]() | ISOMERASE / phosphoglucose isomerase / cupin superfamily / iron ion / archaea / gluconate 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 | ![]() ![]() | ||||||
![]() | Jeong, J.-J. / Fushinobu, S. / Ito, S. / Hidaka, M. / Shoun, H. / Wakagi, T. | ||||||
![]() | ![]() Title: Crystal structure of a novel cupin-type phosphoglucose isomerase Authors: Jeong, J.-J. / Fushinobu, S. / Ito, S. / Hidaka, M. / Shoun, H. / Wakagi, T. #1: Journal: FEBS Lett. / Year: 2003 Title: Characterization of the cupin-type phosphoglucose isomerase from the hyperthermophilic archaeon Thermococcus litoralis(1). Authors: Jeong, J.-J. / Fushinobu, S. / Ito, S. / Jeon, B.-S. / Shoun, H. / Wakagi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 70 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 | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j3pSC ![]() 1j3qC 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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Details | The biological assembly is a dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 21749.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-FE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4 Details: PEG 8000, potassium phosphate, gluconate 6-phosphate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 30, 2002 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→40.12 Å / Num. all: 22995 / Num. obs: 22995 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 7.06 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.1 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J3P Resolution: 2.18→40.11 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1458307.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 79.3442 Å2 / ksol: 0.449829 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.18→40.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.32 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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