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Yorodumi- PDB-2y8r: Crystal structure of apo AMA1 mutant (Tyr230Ala) from Toxoplasma ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y8r | ||||||
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Title | Crystal structure of apo AMA1 mutant (Tyr230Ala) from Toxoplasma gondii | ||||||
Components | APICAL MEMBRANE ANTIGEN, PUTATIVE | ||||||
Keywords | MEMBRANE PROTEIN / MOVING JUNCTION / INVASION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TOXOPLASMA GONDII (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Tonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / Boulanger, M.J. | ||||||
Citation | Journal: Science / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y8r.cif.gz | 323.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y8r.ent.gz | 267.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y8r_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
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Full document | 2y8r_full_validation.pdf.gz | 540 KB | Display | |
Data in XML | 2y8r_validation.xml.gz | 66.1 KB | Display | |
Data in CIF | 2y8r_validation.cif.gz | 91 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y8r ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y8r | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 47921.363 Da / Num. of mol.: 4 / Fragment: DOMAINS I/II/III, RESIDUES 64-484 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: B9QC59, UniProt: B6KAM0*PLUS #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 230 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 230 TO ALA ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.89 % / Description: NONE |
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Crystal grow | Details: 21% PEG3350, 100 MM TRIS PH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 |
Detector | Type: MARMOSAIC 325 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: 2.35→38.59 Å / Num. obs: 63415 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 96.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→38.59 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.839 / SU B: 13.133 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 2.724 / ESU R Free: 0.382 / 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: 28.849 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→38.59 Å
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Refine LS restraints |
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