+Open data
-Basic information
Entry | Database: PDB / ID: 4apl | ||||||
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Title | Crystal Structure of AMA1 from Neospora caninum | ||||||
Components | APICAL MEMBRANE ANTIGEN 1 | ||||||
Keywords | MEMBRANE PROTEIN / APICOMPLEXA / MOVING JUNCTION / INVASION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NEOSPORA CANINUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tonkin, M.L. / Crawford, J. / Lebrun, M.L. / Boulanger, M.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: Babesia Divergens and Neospora Caninum Apical Membrane Antigen 1 (Ama1) Structures Reveal Selectivity and Plasticity in Apicomplexan Parasite Host Cell Invasion. Authors: Tonkin, M.L. / Crawford, J. / Lebrun, M.L. / 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 | 4apl.cif.gz | 315.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4apl.ent.gz | 256.8 KB | Display | PDB format |
PDBx/mmJSON format | 4apl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4apl_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 4apl_full_validation.pdf.gz | 518.6 KB | Display | |
Data in XML | 4apl_validation.xml.gz | 59.1 KB | Display | |
Data in CIF | 4apl_validation.cif.gz | 79.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/4apl ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4apl | HTTPS FTP |
-Related structure data
Related structure data | 4apmC 2x2zS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 47993.102 Da / Num. of mol.: 4 / Fragment: DOMAINS I/II/III, RESIDUES 59-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEOSPORA CANINUM (eukaryote) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A2A114 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % / Description: NONE |
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Crystal grow | Details: 20% PEG3350, 300 MM SODIUM CITRATE PH 4.2 AND 10 MM ZINC CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 |
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: 2.9→50 Å / Num. obs: 41269 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 96.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X2Z Resolution: 2.9→48.44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.861 / SU B: 16.873 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.656 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→48.44 Å
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Refine LS restraints |
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