+Open data
-Basic information
Entry | Database: PDB / ID: 1k3d | ||||||
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Title | Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3 | ||||||
Components | Phosphoenolpyruvate carboxykinase | ||||||
Keywords | LYASE / Kinase / gluconeogenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sudom, A.M. / Prasad, L. / Goldie, H. / Delbaere, L.T.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3). Authors: Sudom, A.M. / Prasad, L. / Goldie, H. / Delbaere, L.T. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: TAKEN FROM PDB ENTRY 1AQ2. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: TAKEN FROM PDB ENTRY 1AQ2. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k3d.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k3d.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 1k3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k3d_validation.pdf.gz | 785.6 KB | Display | wwPDB validaton report |
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Full document | 1k3d_full_validation.pdf.gz | 794.9 KB | Display | |
Data in XML | 1k3d_validation.xml.gz | 24 KB | Display | |
Data in CIF | 1k3d_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k3d ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k3d | HTTPS FTP |
-Related structure data
Related structure data | 1k3cC 1aq2S 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
#1: Protein | Mass: 59709.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / 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 | ChemComp-ADP / |
#4: Chemical | ChemComp-AF3 / |
#5: 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: 2.34 Å3/Da / Density % sol: 47.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: ADP, Aluminum Nitrate, Magnesium Chloride, Sodium Fluoride, EDTA, ammonium acetate, sodium acetate buffer, dithiothreitol, PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 14, 1998 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 35758 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.071 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 87.1 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 96 % / Redundancy: 3.07 % / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1AQ2 Resolution: 2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 23.4 |