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- PDB-2y8t: Co-structure of AMA1 with a surface exposed region of RON2 from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y8t | ||||||
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Title | Co-structure of AMA1 with a surface exposed region of RON2 from Toxoplasma gondii | ||||||
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![]() | MEMBRANE PROTEIN / MOVING JUNCTION / INVASION | ||||||
Function / homology | ![]() host cell plasma membrane / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / Boulanger, M.J. | ||||||
![]() | ![]() Title: Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of Ama1 with a Ron2 Peptide Authors: Tonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / 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 | ![]() | 195.4 KB | Display | ![]() |
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PDB format | ![]() | 152.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.7 KB | Display | ![]() |
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Full document | ![]() | 526.1 KB | Display | |
Data in XML | ![]() | 41.6 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y8rC ![]() 2y8sC ![]() 2x2zS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48013.457 Da / Num. of mol.: 2 / Fragment: DOMAINS I/II/III, RESIDUES 64-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3752.296 Da / Num. of mol.: 2 / Fragment: RESIDUES 235-271 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | AMIDATED THREONINE (9AT): AMIDATED C-TERMINAL THREONINE | Sequence details | FOR CHAINS B AND E AUTHOR HAS PROVIDED A GENBANK REFERENCE HQ110093. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.57 % / Description: NONE |
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Crystal grow | Details: 25% PEG 1500, 100 MM MIB PH 4.0 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45 Å / Num. obs: 68179 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9 |
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Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X2Z Resolution: 1.95→39.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.347 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.694 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→39.81 Å
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Refine LS restraints |
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