+Open data
-Basic information
Entry | Database: PDB / ID: 7ufq | ||||||
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Title | Structure of PfCSP peptide 21 with antibody P3-43 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Malaria / Circumsporozoite | ||||||
Function / homology | Function and homology information entry into host cell by a symbiont-containing vacuole / side of membrane / cell surface / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tripathi, P. / Kwong, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of PfCSP peptide 21 with antibody P3-43 Authors: Tripathi, P. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ufq.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ufq.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ufq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/7ufq ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7ufq | HTTPS FTP |
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-Related structure data
Related structure data | 6b5mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Antibody | Mass: 24207.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Protein/peptide | Mass: 1562.553 Da / Num. of mol.: 2 / Fragment: Junctional peptide 21 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P02893 #3: Antibody | Mass: 24229.838 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 | ChemComp-GOL / | #5: Water | ChemComp-HOH / | 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: 1.99 Å3/Da / Density % sol: 38.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris hydrochloride pH 8.5, 2.25 M Ammonium hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.52 Å / Num. obs: 34697 / % possible obs: 97.45 % / Redundancy: 3.4 % / CC1/2: 0.984 / Net I/σ(I): 8.92 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 3381 / CC1/2: 0.587 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6b5m Resolution: 2.3→43.52 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.17 / 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: 75.88 Å2 / Biso mean: 33.6841 Å2 / Biso min: 13.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→43.52 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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