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Yorodumi- PDB-5ok0: Structure of the D10N mutant of beta-phosphoglucomutase from Lact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ok0 | |||||||||
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Title | Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / phosphoglucomutase / bisphospho-intermediate | |||||||||
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: 2.15 Å | |||||||||
Authors | Robertson, A.J. / Bisson, C. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Acs Catalysis / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ok0.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ok0.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 5ok0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/5ok0 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5ok0 | HTTPS FTP |
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-Related structure data
Related structure data | 5o6pC 5o6rC 5ojzC 5ok1C 5ok2C 2wf5S S: Starting model for refinement C: citing same article (ref.) |
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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: 23852.119 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, D10N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase |
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#2: Sugar | ChemComp-B16 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-PDO / |
#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: 2.19 Å3/Da / Density % sol: 43.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 24-34% PEG 4000 200mM Tris pH 7.5 200mM sodium acetate harvested after 1 week PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.51 Å / Num. obs: 11990 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.98 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.148 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.683 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 598 / CC1/2: 0.391 / Rpim(I) all: 0.721 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WF5 Resolution: 2.15→48.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.097 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 31.793 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→48.51 Å
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Refine LS restraints |
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