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- PDB-4c4r: Structure of beta-phosphoglucomutase in complex with a phosphonat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c4r | ||||||
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Title | Structure of beta-phosphoglucomutase in complex with a phosphonate analogue of beta-glucose-1-phosphate and magnesium trifluoride | ||||||
![]() | BETA-PHOSPHOGLUCOMUTASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pellegrini, E. / Bowler, M.W. | ||||||
![]() | ![]() Title: Alpha-Fluorophosphonates Reveal How a Phosphomutase Conserves Transition State Conformation Over Hexose Recognition in its Two-Step Reaction. Authors: Jin, Y. / Bhattasali, D. / Pellegrini, E. / Forget, S.M. / Baxter, N.J. / Cliff, M.J. / Bowler, M.W. / Jakeman, D.L. / Blackburn, G.M. / Waltho, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.5 KB | Display | ![]() |
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PDB format | ![]() | 94.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wf7C ![]() 4c4sC ![]() 4c4tC ![]() 2wf5S C: citing same article ( S: Starting model for refinement |
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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: 24239.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Sugar | ChemComp-YO5 / ( |
#4: Chemical | ChemComp-MGF / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.3 % / Description: NONE |
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Crystal grow![]() | pH: 7.2 Details: 27-32% PEG 4000, 50-75 MM MAGNESIUM ACETATE, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2012 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.1→52.7 Å / Num. obs: 82900 / % possible obs: 93.1 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Biso Wilson estimate: 5.37 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.9 / % possible all: 85.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2WF5 Resolution: 1.1→19.648 Å / SU ML: 0.1 / σ(F): 1.35 / Phase error: 14.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.384 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→19.648 Å
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Refine LS restraints |
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LS refinement shell |
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