+Open data
-Basic information
Entry | Database: PDB / ID: 1ayl | ||||||
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Title | PHOSPHOENOLPYRUVATE CARBOXYKINASE | ||||||
Components | PHOSPHOENOLPYRUVATE CARBOXYKINASE | ||||||
Keywords | KINASE (TRANSPHOSPHORYLATING) / P-LOOP / PROTEIN-ATP COMPLEX / NUCLEOTIDE-TRIPHOSPHATE HYDROLASE | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Tari, L.W. / Pugazenthi, U. / Goldie, H. / Delbaere, L.T.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase. Authors: Tari, L.W. / Matte, A. / Pugazhenthi, U. / Goldie, H. / Delbaere, L.T. #1: Journal: To be Published Title: Allosteric Control by Calcium and Mechanism of Desensitization of Phosphoenolpyruvate Carboxykinase of Escherichia Coli Authors: Goldie, H. / Sanwal, B.D. #2: Journal: J.Mol.Biol. / Year: 1996 Title: Crystal Structure of Escherichia Coli Phosphoenolpyruvate Carboxykinase: A New Structural Family with the P-Loop Nucleoside Triphosphate Hydrolase Fold Authors: Matte, A. / Goldie, H. / Sweet, R.M. / Delbaere, L.T. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization of the Calcium-Activated Phosphoenolpyruvate Carboxykinase from Escherichia Coli K12 Authors: Delbaere, L.T. / Vandonselaar, M. / Glaeske, D. / Jabs, C. / Goldie, H. #4: Journal: J.Bacteriol. / Year: 1990 Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma ...Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma Brucei and Saccharomyces Cerevisiae Authors: Medina, V. / Pontarollo, R. / Glaeske, D. / Tabel, 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 | 1ayl.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayl.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 1ayl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayl ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59796.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ORDERED MAGNESIUM ION OBSERVED BOUND TO ATP / Source: (natural) Escherichia coli (E. coli) / Strain: K12 References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP) |
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#2: Chemical | ChemComp-OXL / |
#3: Chemical | ChemComp-MG / |
#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: 2.4 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
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Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Num. obs: 40067 / % possible obs: 76.7 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.076 |
Reflection | *PLUS Highest resolution: 1.8 Å |
-Processing
Software |
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Refinement | Resolution: 1.8→6 Å / σ(F): 2 Details: MET 477 HAS DISALLOWED RAMACHANDRAN ANGLES; THE DEPOSITORS ACCOUNT FOR THIS AS IT IS THE SECOND RESIDUE WITHIN A GAMMA-TURN.
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Displacement parameters | Biso mean: 21.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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