+Open data
-Basic information
Entry | Database: PDB / ID: 7raj | ||||||
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Title | Structure of PfCSP peptide 21 with antibody iGL-CIS43.D3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Plasmodium falciparum | ||||||
Biological species | Homo sapiens (human) Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Tripathi, P. / Kwong, P.D. | ||||||
Funding support | 1items
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Citation | Journal: Immunity / Year: 2021 Title: Vaccination in a humanized mouse model elicits highly protective PfCSP-targeting anti-malarial antibodies. Authors: Kratochvil, S. / Shen, C.H. / Lin, Y.C. / Xu, K. / Nair, U. / Da Silva Pereira, L. / Tripathi, P. / Arnold, J. / Chuang, G.Y. / Melzi, E. / Schon, A. / Zhang, B. / Dillon, M. / Bonilla, B. / ...Authors: Kratochvil, S. / Shen, C.H. / Lin, Y.C. / Xu, K. / Nair, U. / Da Silva Pereira, L. / Tripathi, P. / Arnold, J. / Chuang, G.Y. / Melzi, E. / Schon, A. / Zhang, B. / Dillon, M. / Bonilla, B. / Flynn, B.J. / Kirsch, K.H. / Kisalu, N.K. / Kiyuka, P.K. / Liu, T. / Ou, L. / Pancera, M. / Rawi, R. / Reveiz, M. / Seignon, K. / Wang, L.T. / Waring, M.T. / Warner, J. / Yang, Y. / Francica, J.R. / Idris, A.H. / Seder, R.A. / Kwong, P.D. / Batista, F.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7raj.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7raj.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 7raj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7raj_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 7raj_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 7raj_validation.xml.gz | 18 KB | Display | |
Data in CIF | 7raj_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/7raj ftp://data.pdbj.org/pub/pdb/validation_reports/ra/7raj | HTTPS FTP |
-Related structure data
Related structure data | 7lkbC 7lkgC 7rcsC 7rd3C 7rd4C 7rd9C 7rdaC 6b5lS S: Starting model for refinement 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
-Protein/peptide , 1 types, 1 molecules A
#3: Protein/peptide | Mass: 1562.553 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24245.312 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: 24247.854 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 , 3 types, 5 molecules
#4: Chemical | ChemComp-MES / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M Zn acetate, 0.1 M MES, 17.53% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→36.79 Å / Num. obs: 9207 / % possible obs: 97.19 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3→3.107 Å / Num. unique obs: 859 / CC1/2: 0.717 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B5L Resolution: 3→36.79 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 87.94 Å2 / Biso mean: 58.6783 Å2 / Biso min: 45.77 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→36.79 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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