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Yorodumi- PDB-2py7: Crystal structure of E. coli phosphoenolpyruvate carboxykinase mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2py7 | ||||||
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Title | Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+ | ||||||
Components | Phosphoenolpyruvate carboxykinase | ||||||
Keywords | LYASE / phosphoenolpyruvate carboxykinase / active site lysine / tetrahedral manganese coordination | ||||||
Function / homology | Function and homology information phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Delbaere, L.T.J. / Cotelesage, J.J.H. / Goldie, H. | ||||||
Citation | Journal: To be Published Title: Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser Authors: Delbaere, L.T.J. / Cotelesage, J.J.H. / Goldie, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2py7.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2py7.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 2py7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/2py7 ftp://data.pdbj.org/pub/pdb/validation_reports/py/2py7 | HTTPS FTP |
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-Related structure data
Related structure data | 1aylS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 59667.074 Da / Num. of mol.: 1 / Mutation: K213S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pckA / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP) | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: A 2ul drop with 4 mg/ml protein, 20 mM Tris-HCl (pH 7.6), 0.5 mM EDTA, 5 mM ADP, 2.5 mM phosphoenolpyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 0.1 M sodium acetate, 0.05 M sodium cacodylate (pH 6. ...Details: A 2ul drop with 4 mg/ml protein, 20 mM Tris-HCl (pH 7.6), 0.5 mM EDTA, 5 mM ADP, 2.5 mM phosphoenolpyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 0.1 M sodium acetate, 0.05 M sodium cacodylate (pH 6.5), 15% PEG 8000 was allowed to equilibrate with a 1 ml well of 0.2 M sodium aceate, 0.1 M sodium cacodylate 30% PEG 8000. After a week a 0.1 x 0.1 x 0.4 mm crystal was removed and put in a small volume of well solution with 30% glycerol added. The crystal was put into a loop and flash cooled in liquid notrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.919 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Diamond (111) double-crystal monochromator Bent cylindrical Si-mirror (Rh coating) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→99 Å / Num. all: 89783 / Num. obs: 36560 / % possible obs: 85.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 13.96 / Redundancy: 2.95 % / Rsym value: 0.1 |
Reflection shell | Resolution: 2.02→2.28 Å / Redundancy: 1.17 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 0 / Rsym value: 0.14 / % possible all: 59.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AYL Resolution: 2.2→18.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.075 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.325 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→18.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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