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- PDB-1qy4: Crystal structure of phosphoglucose isomerase from Pyrococcus fur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qy4 | ||||||
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Title | Crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with gluconate 6-phosphate | ||||||
![]() | Glucose-6-phosphate isomerase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Swan, M.K. / Solomons, J.T.G. / Beeson, C.C. / Hansen, T. / Schonheit, P. / Davies, C. | ||||||
![]() | ![]() Title: Structural evidence for a hydride transfer mechanism of catalysis in phosphoglucose isomerase from Pyrococcus furiosus Authors: Swan, M.K. / Solomons, J.T.G. / Beeson, C.C. / Hansen, T. / Schonheit, P. / Davies, C. #1: ![]() Title: Crystallization and preliminary X-ray diffraction analysis of phosphoglucose isomerase from Pyrococcus furiosus Authors: Swan, M.K. / Hansen, T. / Schonheit, P. / Davies, C. | ||||||
History |
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Remark 600 | HETEROGEN The carboxylate oxygens of gluconate 6-phosphate are labeled O1 and O1A in the PDB file ...HETEROGEN The carboxylate oxygens of gluconate 6-phosphate are labeled O1 and O1A in the PDB file whereas in the published paper describing this structure these atoms are referred to as O1A and O1B, respectively. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.2 KB | Display | ![]() |
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PDB format | ![]() | 70.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qxjSC ![]() 1qxrC 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: 21505.436 Da / Num. of mol.: 2 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: 2.3 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 4000, 0.2M ammonium acetate, 0.1 M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 5, 2003 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→36.8 Å / Num. obs: 32924 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3174 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 89107 |
Reflection shell | *PLUS % possible obs: 90.9 % |
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Processing
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Refinement | Method to determine structure![]() Starting model: PDB entry 1QXJ Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.533 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.162 / 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: 33.652 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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