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Open data
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Basic information
Entry | Database: PDB / ID: 2xgg | ||||||
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Title | Structure of Toxoplasma gondii Micronemal Protein 2 A_I Domain | ||||||
![]() | MICRONEME PROTEIN 2 | ||||||
![]() | HYDROLASE / MICRONEME / MIC2 / A/I DOMAIN / CELL ADHESION | ||||||
Function / homology | von Willebrand factor, type A domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tonkin, M.L. / Grujic, O. / Pearce, M. / Crawford, J. / Boulanger, M.J. | ||||||
![]() | ![]() Title: Structure of the Micronemal Protein 2 (Mic2) A/I Domain from Toxoplasma Gondii. Authors: Tonkin, M.L. / Grujic, O. / Pearce, M. / Crawford, J. / 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 | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.9 KB | Display | ![]() |
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Full document | ![]() | 461.5 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components
#1: Protein | Mass: 19309.014 Da / Num. of mol.: 2 / Fragment: VWA INTEGRIN-LIKE DOMAIN, RESIDUES 26-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.6 % / Description: NONE |
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Crystal grow | Details: 27% PEG3350, 0.1M HEPES 7.5, 0.2M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→24.84 Å / Num. obs: 20754 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.69 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 10.82 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.5.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.05→24.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.173 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED BASED ON OVERLAYS WITH THE ALTERNATE CHAIN AND STEREOCHEMISTRY.
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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: 44.097 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→24.84 Å
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