+Open data
-Basic information
Entry | Database: PDB / ID: 6v2l | |||||||||
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Title | E. coli Phosphoenolpyruvate carboxykinase S250A | |||||||||
Components | Phosphoenolpyruvate carboxykinase (ATP)Phosphoenolpyruvate carboxykinase (ATP) | |||||||||
Keywords | LYASE | |||||||||
Function / homology | Function and homology information phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / kinase activity / calcium ion binding / magnesium ion binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Sokaribo, A.S. / Goldie, H. / Sanders, D. | |||||||||
Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2020 Title: Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants. Authors: Sokaribo, A. / Novakovski, B.A.A. / Cotelesage, J. / White, A.P. / Sanders, D. / Goldie, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v2l.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v2l.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/6v2l ftp://data.pdbj.org/pub/pdb/validation_reports/v2/6v2l | HTTPS FTP |
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-Related structure data
Related structure data | 6comC 6v2mC 6v2nC 1aylS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 59739.270 Da / Num. of mol.: 1 / Mutation: S250A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pckA, D9G24_04840 / Production host: Escherichia coli (E. coli) References: UniProt: A0A400L9R1, UniProt: P22259*PLUS, phosphoenolpyruvate carboxykinase (ATP) | ||||
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#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: A 2ul drop with 3 mg/ml S250A PCK, 5 mM Manganese chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate pH 4.8, 0.01 mM DTT, 12% ...Details: A 2ul drop with 3 mg/ml S250A PCK, 5 mM Manganese chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate pH 4.8, 0.01 mM DTT, 12% PEG 4000 was added to 2 ul drop containing 0.01 mM Nickel chloride, 0.1 M Tris pH 8.5, 20% PEG 2000. After a week a rod like crystal was removed and soaked in a solution with 30% glycerol 1mM EDTA, 100 mM sodium acetate 200mM ammonium acetate and 12% PEG 4000 for 10 seconds and flash cooled in liquid notrogen |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.8856 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40.5 Å / Num. obs: 58603 / % possible obs: 99.59 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.05 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1803 / Rpim(I) all: 0.1056 / Rrim(I) all: 0.2092 / Net I/σ(I): 9.63 |
Reflection shell | Resolution: 1.7→1.761 Å / Rmerge(I) obs: 1.237 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 5814 / CC1/2: 0.491 / Rpim(I) all: 0.7255 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AYL Resolution: 1.7→40.5 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.41 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.42 Å2 / Biso mean: 21.3601 Å2 / Biso min: 9.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→40.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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