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Yorodumi- PDB-4c4r: Structure of beta-phosphoglucomutase in complex with a phosphonat... -
+Open data
-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 | ||||||
Components | BETA-PHOSPHOGLUCOMUTASE | ||||||
Keywords | ISOMERASE / PHOSPHORYL TRANSFER / TRANSITION STATE / METAL FLUORIDE / MUTASE | ||||||
Function / homology | Function and homology information beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | LACTOCOCCUS LACTIS (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Pellegrini, E. / Bowler, M.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c4r.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c4r.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 4c4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c4r ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c4r | HTTPS FTP |
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-Related structure data
Related structure data | 2wf7C 4c4sC 4c4tC 2wf5S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 24239.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
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: 0.976 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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