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Yorodumi- PDB-3umo: Crystal structure of the Phosphofructokinase-2 from Escherichia c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3umo | ||||||
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Title | Crystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with Potassium | ||||||
Components | 6-phosphofructokinase isozyme 2 | ||||||
Keywords | TRANSFERASE / GLYCOLYSIS / PFK / enzyme | ||||||
Function / homology | Function and homology information tagatose-6-phosphate kinase activity / 6-phosphofructokinase / 6-phosphofructokinase activity / glycolytic process / DNA damage response / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.696 Å | ||||||
Authors | Pereira, H.M. / Caniuguir, A. / Baez, M. / Cabrera, R. / Garratt, R.C. / Babul, J. | ||||||
Citation | Journal: Biophys.J. / Year: 2013 Title: A Ribokinase Family Conserved Monovalent Cation Binding Site Enhances the MgATP-induced Inhibition in E. coli Phosphofructokinase-2 Authors: Baez, M. / Cabrera, R. / Pereira, H.M. / Blanco, A. / Villalobos, P. / Ramirez-Sarmiento, C.A. / Caniuguir, A. / Guixe, V. / Garratt, R.C. / Babul, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3umo.cif.gz | 258 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3umo.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 3umo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/3umo ftp://data.pdbj.org/pub/pdb/validation_reports/um/3umo | HTTPS FTP |
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-Related structure data
Related structure data | 3umpC 3cqdS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32486.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1723, JW5280, PFK2, pfkB / Plasmid: PET21-D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06999, 6-phosphofructokinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ATP / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.75 Details: 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2010 / Details: DCM Si(311) and Si(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(311) AND SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.696→50 Å / Num. all: 77204 / Num. obs: 76251 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.02 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.06 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CQD Resolution: 1.696→48.967 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.48 / σ(F): 2.02 / Phase error: 19.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.314 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.65 Å2 / Biso mean: 30.7992 Å2 / Biso min: 10.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.696→48.967 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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