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Yorodumi- PDB-5ojz: D10N variant of beta-phosphoglucomutase from Lactococcus lactis i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ojz | |||||||||
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Title | D10N variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by a beryllium triflouride phosphoenzyme analogue to 1.3A resolution. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / phosphoglucomutase / phosphoenzyme analogue | |||||||||
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: 1.3 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 | 5ojz.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ojz.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ojz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ojz_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 5ojz_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 5ojz_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5ojz_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojz ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojz | HTTPS FTP |
-Related structure data
Related structure data | 5o6pC 5o6rC 5ok0C 5ok1C 5ok2C 2wheS 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: 24109.430 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) Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BEF / | #4: Chemical | ChemComp-EDO / #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: 2.4 Å3/Da / Density % sol: 48.76 % |
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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 PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→44.3 Å / Num. obs: 57228 / % possible obs: 99 % / Redundancy: 16.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2525 / CC1/2: 0.489 / Rpim(I) all: 0.542 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WHE Resolution: 1.3→44.3 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.793 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / 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: 19.59 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→44.3 Å
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Refine LS restraints |
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