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Open data
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Basic information
Entry | Database: PDB / ID: 7phw | ||||||
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Title | PfCyRPA bound to monoclonal antibody Cy.004 Fab fragment | ||||||
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![]() | IMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine | ||||||
Function / homology | ![]() microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ragotte, R.J. / Higgins, M.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Heterotypic interactions drive antibody synergy against a malaria vaccine candidate. Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / ...Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / Bowyer, P.W. / Higgins, M.K. / Draper, S.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 | ![]() | 598.6 KB | Display | ![]() |
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PDB format | ![]() | 492.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 873.9 KB | Display | ![]() |
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Full document | ![]() | 898.1 KB | Display | |
Data in XML | ![]() | 50.3 KB | Display | |
Data in CIF | ![]() | 69.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7phuC ![]() 7phvC ![]() 7pi2C ![]() 7pi3C ![]() 7pi7C ![]() 5tihS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40184.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: CyRPA, pfd1130w, PF3D7_0423800 / Production host: ![]() #2: Antibody | Mass: 34168.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 22451.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 6000, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→47.11 Å / Num. obs: 284862 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.79→2.87 Å / Num. unique obs: 13827 / CC1/2: 0.757 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TIH Resolution: 2.793→47.11 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.392
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Displacement parameters | Biso max: 176.5 Å2 / Biso mean: 90.11 Å2 / Biso min: 43.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.44 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.793→47.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.793→2.82 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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