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- PDB-5j3u: Co-crystal structure of the regulatory domain of Toxoplasma gondi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j3u | ||||||
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Title | Co-crystal structure of the regulatory domain of Toxoplasma gondii PKA with cAMP | ||||||
![]() | Protein Kinase A![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | El Bakkouri, M. / Walker, J.R. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lin, L. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Co-crystal structure of the regulatory domain of Toxoplasma gondii PKA with cAMP Authors: El Bakkouri, M. / Walker, J.R. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lin, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 54.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 28950.900 Da / Num. of mol.: 1 / Fragment: regulatory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: S8EY88, UniProt: A0A0F7V8B2*PLUS, ![]() | ||||
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#2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.17 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% peg3350, 0.1M NH4Oac, 0.1M Hepes pH 7.5, 2 mM cAMP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection | Resolution: 1.8→42.36 Å / Num. obs: 25458 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.034 / Rrim(I) all: 0.101 / Net I/σ(I): 19.2 / Num. measured all: 221793 | |||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 3OF1, 2QCS, 3TNP Resolution: 1.8→41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.817 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.119 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.94 Å2 / Biso mean: 22.494 Å2 / Biso min: 5.45 Å2
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Refinement step | Cycle: final / Resolution: 1.8→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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