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- PDB-4u0r: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u0r | ||||||
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Title | Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to monoclonal antibody 9AD4 | ||||||
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![]() | IMMUNE SYSTEM / malaria erythrocyte invasion antibody-mediated inhibition | ||||||
Function / homology | Rh5 coiled-coil domain / Rh5 coiled-coil domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Reticulocyte binding protein 5![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K. | ||||||
![]() | ![]() Title: Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies. Authors: Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Illingworth, J.J. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.5 KB | Display | ![]() |
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PDB format | ![]() | 250 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460 KB | Display | ![]() |
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Full document | ![]() | 476.3 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u0qC ![]() 4u1gC ![]() 3hr5S ![]() 3qq9S 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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Unit cell |
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Components
#1: Protein | Mass: 63128.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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#2: Antibody | Mass: 27641.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 26259.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 1500, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41.86 Å / Num. obs: 49434 / % possible obs: 96.2 % / Redundancy: 5 % / Biso Wilson estimate: 48.97 Å2 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2 / % possible all: 83.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QQ9, 3HR5 Resolution: 2.3→40.83 Å / Cor.coef. Fo:Fc: 0.9086 / Cor.coef. Fo:Fc free: 0.8801 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.236 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.206
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Displacement parameters | Biso mean: 54.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.392 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→40.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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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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