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- PDB-4yiz: Crystal structure of engineered TgAMA1 lacking the DII loop in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yiz | |||||||||
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Title | Crystal structure of engineered TgAMA1 lacking the DII loop in complex with an Eimeria tenella RON2D3 peptide | |||||||||
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![]() | IMMUNE SYSTEM / Apicomplexa / invasion / moving junction / parasite / protein engineering / PAN domain | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Parker, M.L. / Boulanger, M.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An Extended Surface Loop on Toxoplasma gondii Apical Membrane Antigen 1 (AMA1) Governs Ligand Binding Selectivity. Authors: Parker, M.L. / Boulanger, M.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 274 KB | Display | ![]() |
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PDB format | ![]() | 220.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.1 KB | Display | ![]() |
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Full document | ![]() | 523.7 KB | Display | |
Data in XML | ![]() | 48.5 KB | Display | |
Data in CIF | ![]() | 68.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yivC ![]() 2y8tS C: citing same article ( 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 46064.297 Da / Num. of mol.: 3 / Fragment: residues 64-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3872.359 Da / Num. of mol.: 3 / Fragment: residues 1261-1285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/A2G.gif)
![](data/chem/img/A2G.gif)
#3: Sugar | #4: Sugar | ChemComp-A2G / | |
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-Non-polymers , 2 types, 492 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | The authors state that the twenty flexible residues of the DII loop (HTYPLTSQASWNDWWPLHQS) were ...The authors state that the twenty flexible residues of the DII loop (HTYPLTSQAS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.42 Å3/Da / Density % sol: 80.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M tri-sodium citrate pH 5.0 and 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→72.89 Å / Num. obs: 180412 / % possible obs: 93.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.4 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 2Y8T Resolution: 2.2→59.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→59.5 Å
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Refine LS restraints |
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LS refinement shell |
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