+Open data
-Basic information
Entry | Database: PDB / ID: 8pwx | ||||||
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Title | PfRH5 bound to monoclonal antibody R5.008 | ||||||
Components |
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Keywords | CELL ADHESION / Plasmodium falciparum / malaria / monoclonal antibody / growth-inhibition / blood stage / erythrocyte invasion | ||||||
Function / homology | Function and homology information rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding ...rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding / host cell plasma membrane / protein-containing complex / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Farrell, B. / Higgins, M.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: PfRH5 bound to monoclonal antibody R5.008 Authors: Farrell, B. / Higgins, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pwx.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pwx.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pwx_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 8pwx_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 8pwx_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 8pwx_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/8pwx ftp://data.pdbj.org/pub/pdb/validation_reports/pw/8pwx | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 29732.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Protein | Mass: 40962.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: RH5, PFD1145c, PF3D7_0424100 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IFM5 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.12 M Ethylene Glycol Mix (di-, tri-, tetra- and pentaethylene glycols) 0.1 M Buffer System 3 pH 8.5 (BICINE, Trizma base) 30% v/v Precipitant Mix 3 (glycerol, PEG 4000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→57.49 Å / Num. obs: 19138 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 75.45 Å2 / CC1/2: 0.986 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.2→3.42 Å / Num. unique obs: 3408 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.79 Å / SU ML: 0.4561 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.8308 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→49.79 Å
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Refine LS restraints |
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LS refinement shell |
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