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Yorodumi- PDB-3n1c: Crystal structure of the phosphofructokinase-2 from Escherichia c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n1c | ||||||
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Title | Crystal structure of the phosphofructokinase-2 from Escherichia coli in complex with fructose-6-phosphate | ||||||
Components | 6-phosphofructokinase isozyme 2 | ||||||
Keywords | TRANSFERASE / Phosphofructokinases / Pfk-2 / Escherichia coli / Glycolysis | ||||||
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: 2 Å | ||||||
Authors | Pereira, H.M. / Cabrera, R. / Caniuguir, A. / Garratt, R.C. / Babul, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Crystal Complex of Phosphofructokinase-2 of Escherichia coli with Fructose-6-phosphate: KINETIC AND STRUCTURAL ANALYSIS OF THE ALLOSTERIC ATP INHIBITION. Authors: Cabrera, R. / Baez, M. / Pereira, H.M. / Caniuguir, A. / 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 | 3n1c.cif.gz | 490.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n1c.ent.gz | 405.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/3n1c ftp://data.pdbj.org/pub/pdb/validation_reports/n1/3n1c | HTTPS FTP |
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-Related structure data
Related structure data | 3cqdS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32486.900 Da / Num. of mol.: 4 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: Sugar | ChemComp-F6P / #3: 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: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 291 K / 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: LNLS / Beamline: W01B-MX2 / Wavelength: 1.43 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.43 Å / Relative weight: 1 |
Reflection | Resolution: 2→111.895 Å / Num. obs: 79638 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.508 / % possible all: 97.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 44.05 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CQD Resolution: 2→36.45 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.28 / σ(F): 0.02 / Phase error: 21.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→36.45 Å
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Refine LS restraints |
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LS refinement shell |
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