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- PDB-1ii2: Crystal Structure of Phosphoenolpyruvate Carboxykinase (PEPCK) fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ii2 | ||||||
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Title | Crystal Structure of Phosphoenolpyruvate Carboxykinase (PEPCK) from Trypanosoma cruzi | ||||||
![]() | PHOSPHOENOLPYRUVATE CARBOXYKINASE | ||||||
![]() | LYASE / Phosphate binding loop | ||||||
Function / homology | ![]() phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / glycosome / gluconeogenesis / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trapani, S. / Linss, J. / Goldenberg, S. / Fischer, H. / Craievich, A.F. / Oliva, G. | ||||||
![]() | ![]() Title: Crystal structure of the dimeric phosphoenolpyruvate carboxykinase (PEPCK) from Trypanosoma cruzi at 2 A resolution. Authors: Trapani, S. / Linss, J. / Goldenberg, S. / Fischer, H. / Craievich, A.F. / Oliva, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.4 KB | Display | ![]() |
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PDB format | ![]() | 180.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 45.4 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aq2S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly in the asymmetric unit is a dimer |
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Components
#1: Protein | Mass: 58816.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P51058, phosphoenolpyruvate carboxykinase (GTP) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Ammonium sulphate, sodium chloride, HEPES, potassium dihydrogen phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6.7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 2000 Details: cylindrically curved mirror for vertical focus; bent Si monochromator for horizontal focus |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.535 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 87770 / Num. obs: 87770 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 4.9 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 4.8 % / Num. unique all: 8629 / Rsym value: 30.1 / % possible all: 99.2 |
Reflection | *PLUS Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 99.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.337 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AQ2 Resolution: 2→21.67 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2445774.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.98 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→21.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.272 / % reflection Rfree: 5 % / Rfactor Rwork: 0.221 |