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- PDB-5o6p: Structure of beta-phosphoglucomutase D10N mutant in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o6p | ||||||
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Title | Structure of beta-phosphoglucomutase D10N mutant in complex with glucose-1,6-bisphosphate | ||||||
![]() | Beta-phosphoglucomutase | ||||||
![]() | ISOMERASE / phosphoryl transfer / catalysis / near attack complex | ||||||
Function / homology | ![]() beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bowler, M.W. | ||||||
![]() | ![]() Title: van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture Authors: Johnson, L.A. / Robertson, A.J. / Baxter, N.J. / Trevitt, C.R. / Bisson, C. / Jin, Y. / Wood, H.P. / Hounslow, A.M. / Cliff, M.J. / Blackburn, G.M. / Bowler, M.W. / 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 | ![]() | 99 KB | Display | ![]() |
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PDB format | ![]() | 74.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.6 KB | Display | ![]() |
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Full document | ![]() | 780.9 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o6rC ![]() 5ojzC ![]() 5ok0C ![]() 5ok1C ![]() 5ok2C ![]() 2wf9S 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: 24238.609 Da / Num. of mol.: 1 / Mutation: D10N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: ![]() ![]() |
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#2: Sugar | ChemComp-B16 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.93 % Description: small needles with approximate dimensions 0.03 mm x 0.05 mm x 0.5 mm |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 28-32 % PEG 4000 and 100 mM Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2009 / Details: toroidla mirror |
Radiation | Monochromator: C001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 31189 / % possible obs: 98.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / Num. unique obs: 4563 / Rpim(I) all: 0.17 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2wf9 Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.032 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.635 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→20 Å
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Refine LS restraints |
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