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Yorodumi- PDB-2olr: Crystal structure of Escherichia coli phosphoenolpyruvate carboxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2olr | ||||||
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Title | Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase complexed with carbon dioxide, Mg2+, ATP | ||||||
Components | Phosphoenolpyruvate carboxykinase | ||||||
Keywords | LYASE / carbon dioxide / carboxykinase | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Cotelesage, J.J. / Delbaere, L.T. / Goldie, H. / Puttick, J. / Rajabi, B. / Novakovski, B. | ||||||
Citation | Journal: Int.J.Biochem.Cell Biol. / Year: 2007 Title: How does an enzyme recognize CO2? Authors: Cotelesage, J.J. / Puttick, J. / Goldie, H. / Rajabi, B. / Novakovski, B. / Delbaere, L.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2olr.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2olr.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 2olr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2olr_validation.pdf.gz | 757 KB | Display | wwPDB validaton report |
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Full document | 2olr_full_validation.pdf.gz | 758.6 KB | Display | |
Data in XML | 2olr_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 2olr_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/2olr ftp://data.pdbj.org/pub/pdb/validation_reports/ol/2olr | HTTPS FTP |
-Related structure data
Related structure data | 2olqC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59709.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: k12 / Gene: pckA, pck / 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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-Non-polymers , 5 types, 459 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Chemical | ChemComp-ATP / | #6: 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: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 8 microL drops: 8 mg/ml protein concentration, 2 mM ATP, 5 mM oxalate, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate, 12% PEG 4000, 1 ml resevoir: 100 mM sodium acetate, 200 mM ...Details: 8 microL drops: 8 mg/ml protein concentration, 2 mM ATP, 5 mM oxalate, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate, 12% PEG 4000, 1 ml resevoir: 100 mM sodium acetate, 200 mM ammonuim acetate, 27% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→75.8 Å / Num. all: 105079 / Num. obs: 105079 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.1 / Num. unique all: 15056 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1AYL Resolution: 1.6→75.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.434 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.085 / 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: 14.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→75.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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