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Yorodumi- PDB-6o26: Crystal structure of 3246 Fab in complex with circumsporozoite pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o26 | ||||||
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Title | Crystal structure of 3246 Fab in complex with circumsporozoite protein NANA | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Malaria / antibody | ||||||
Function / homology | Function and homology information entry into host cell by a symbiont-containing vacuole / external side of plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Scally, S.W. / Bosch, A. / Castro, K. / Murugan, R. / Wardemann, H. / Julien, J.P. | ||||||
Funding support | 1items
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Citation | Journal: Nat. Med. / Year: 2020 Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs. Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o26.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o26.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/6o26 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/6o26 | HTTPS FTP |
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-Related structure data
Related structure data | 6o23C 6o24C 6o25C 6o28C 6o29C 6o2aC 6o2bC 6o2cC 6uleC 6ulfC 6vlnC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1486.482 Da / Num. of mol.: 1 / Fragment: residues 289-302 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P19597 |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23609.465 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: Antibody | Mass: 23324.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Non-polymers , 4 types, 388 molecules
#4: Chemical | ChemComp-TRS / |
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#5: Chemical | ChemComp-EDO / |
#6: Chemical | ChemComp-IPA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 % (v/v) isopropanol, 20 % (w/v) PEG4000, 0.1 M HEPES pH 7.5 and 10 % (w/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 45439 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2139 / CC1/2: 0.532 / Rpim(I) all: 0.302 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.308 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.308 Å
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Refine LS restraints |
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LS refinement shell |
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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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