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- PDB-8dfi: Crystal structure of moderately neutralizing / interfering human ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dfi | ||||||
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Title | Crystal structure of moderately neutralizing / interfering human monoclonal antibody 42C11 Fab in complex with MSP1-19 | ||||||
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![]() | STRUCTURAL PROTEIN/IMMUNE SYSTEM / Merozoite Surface Protein 1 (MSP1) / Antigen-Antibody Complex / Antigenic Diversion / Plasmodium falciparum / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() entry into host cell by a symbiont-containing vacuole / vacuolar membrane / side of membrane / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patel, P.N. / Tang, W.K. / Tolia, N.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Neutralizing and interfering human antibodies define the structural and mechanistic basis for antigenic diversion. Authors: Patel, P.N. / Dickey, T.H. / Hopp, C.S. / Diouf, A. / Tang, W.K. / Long, C.A. / Miura, K. / Crompton, P.D. / Tolia, N.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.8 KB | Display | ![]() |
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PDB format | ![]() | 245.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.6 KB | Display | ![]() |
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Full document | ![]() | 440 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dfgC ![]() 8dfhC ![]() 1aqkS ![]() 1ob1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11759.932 Da / Num. of mol.: 1 / Fragment: UNP residues 1607-1699 / Mutation: S3A, T48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 25667.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23239.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.5, 10 % (w/v) PEG 4000, 20% (w/v) Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.85 Å / Num. obs: 37968 / % possible obs: 94.5 % / Redundancy: 3.45 % / Biso Wilson estimate: 27.26 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.85 |
Reflection shell | Resolution: 1.9→1.95 Å / Mean I/σ(I) obs: 4.86 / Num. unique obs: 2198 / CC1/2: 0.903 / % possible all: 74.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 1OB1 & 1AQK Resolution: 1.9→19.85 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.4991 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 34.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.0717600054 Å / Origin y: 36.7785707262 Å / Origin z: 14.8388203853 Å
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Refinement TLS group | Selection details: all |