+Open data
-Basic information
Entry | Database: PDB / ID: 1aq2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PHOSPHOENOLPYRUVATE CARBOXYKINASE | |||||||||
Components | PHOSPHOENOLPYRUVATE CARBOXYKINASE | |||||||||
Keywords | KINASE / TRANSPHOSPHORYLATING / P-LOOP / PROTEIN-ATP COMPLEX / NUCLEOTIDE-TRIPHOSPHATE HYDROLASE / LYASE / GLUCONEOGENESIS | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Tari, L.W. / Matte, A. / Goldie, H. / Delbaere, L.T.J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Mg(2+)-Mn2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions. Authors: Tari, L.W. / Matte, A. / Goldie, H. / Delbaere, L.T. #1: 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. #2: 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. #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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1aq2.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1aq2.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 1aq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aq2_validation.pdf.gz | 744 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1aq2_full_validation.pdf.gz | 752.1 KB | Display | |
Data in XML | 1aq2_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1aq2_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/1aq2 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/1aq2 | HTTPS FTP |
-Related structure data
Related structure data | 1aylS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 Details: ORDERED MAGNESIUM AND MANGANESE IONS OBSERVED BOUND TO ATP Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 Description: NATIVE PROMOTER OF E. COLI PCKA GENE, HIGHLY AEROBIC GROWTH TO EARLY STATIONARY PHASE IN THE ABSENCE OF CARBOHYDRATES Cellular location: CYTOPLASM / Gene (production host): PCKA / Production host: Escherichia coli (E. coli) References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP) |
---|
-Non-polymers , 5 types, 236 molecules
#2: Chemical | ChemComp-MN / |
---|---|
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
#5: Chemical | ChemComp-PYR / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | pH: 4.4 / Details: pH 4.4 |
-Data collection
Diffraction | Mean temperature: 300 K |
---|---|
Diffraction source | Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 15, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→60 Å / Num. obs: 39324 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rsym value: 0.118 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.9→3 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.34 / % possible all: 85 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AYL Resolution: 1.9→6 Å / Cross valid method: FREE-R / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|