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Yorodumi- PDB-6e63: Crystal structure of malaria transmission-blocking antigen Pfs48/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+63 | ||||||
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Title | Crystal structure of malaria transmission-blocking antigen Pfs48/45 6C in complex with antibody TB31F | ||||||
Components |
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Keywords | IMMUNE SYSTEM / malaria / transmission-blocking / antigen / antibody | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Kundu, P. / Semesi, A. / Julien, J.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural delineation of potent transmission-blocking epitope I on malaria antigen Pfs48/45. Authors: Kundu, P. / Semesi, A. / Jore, M.M. / Morin, M.J. / Price, V.L. / Liang, A. / Li, J. / Miura, K. / Sauerwein, R.W. / King, C.R. / Julien, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e63.cif.gz | 219.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e63.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 6e63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e63 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e63 | HTTPS FTP |
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-Related 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15332.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Homo sapiens (human) / References: UniProt: A8QVT1, UniProt: Q8I6T1*PLUS #2: Antibody | Mass: 23841.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23169.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris, pH 6.0, 22% (w/v) PEG 3350, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.9 Å / Num. obs: 35359 / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3678 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.6→49.899 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→49.899 Å
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Refine LS restraints |
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LS refinement shell |
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