+Open data
-Basic information
Entry | Database: PDB / ID: 4r19 | ||||||
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Title | Crystal Structure of 3D7 strain Plasmodium falciparum AMA1 | ||||||
Components | Apical membrane antigen 1, AMA1 | ||||||
Keywords | CELL INVASION / PAN fold / erythrocyte invasion by merozoites / RON2 / Moving junction complex | ||||||
Function / homology | Function and homology information apical complex / microneme / host cell surface binding / symbiont entry into host / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lim, S.S. / Norton, R.S. / McGowan, S. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO. Authors: Lim, S.S. / Yang, W. / Krishnarjuna, B. / Kannan Sivaraman, K. / Chandrashekaran, I.R. / Kass, I. / MacRaild, C.A. / Devine, S.M. / Debono, C.O. / Anders, R.F. / Scanlon, M.J. / Scammells, P. ...Authors: Lim, S.S. / Yang, W. / Krishnarjuna, B. / Kannan Sivaraman, K. / Chandrashekaran, I.R. / Kass, I. / MacRaild, C.A. / Devine, S.M. / Debono, C.O. / Anders, R.F. / Scanlon, M.J. / Scammells, P.J. / Norton, R.S. / McGowan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r19.cif.gz | 277 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r19.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 4r19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r19_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 4r19_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 4r19_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4r19_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r19 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r19 | HTTPS FTP |
-Related structure data
Related structure data | 4r1aC 4r1bC 4r1cC 1z40S 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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Unit cell |
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-Components
#1: Protein | Mass: 38360.047 Da / Num. of mol.: 2 / Fragment: UNP residues 104-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: AMA1, PF11_0344 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q7KQK5 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12-15 % (v/v) polyethylene glycol 3350, 0.02 M MES and 10 mM manganese chloride. Crystals were dehydrated overnight in reservoir solution with increased (35%) (v/v) polyethylene glycol 3350 ...Details: 12-15 % (v/v) polyethylene glycol 3350, 0.02 M MES and 10 mM manganese chloride. Crystals were dehydrated overnight in reservoir solution with increased (35%) (v/v) polyethylene glycol 3350 before cryo-stabilisation in 38% (v/v) polyethylene glycol 3350, 0.088 M MES (pH 6.0) and 44 mM manganese chloride for 6-8 h prior to data collection, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Monochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.07 Å / Num. obs: 65700 / % possible obs: 100 % / Observed criterion σ(I): 8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z40 Resolution: 1.8→47.07 Å / SU ML: 0.2 / σ(F): 1.96 / Phase error: 20.18 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.132 Å / Origin y: -13.106 Å / Origin z: -7.6224 Å
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Refinement TLS group | Selection details: all |