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- PDB-6w00: Crystal structure of Fab239 in complex with NPNA2 peptide from ci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w00 | ||||||
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Title | Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein | ||||||
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![]() | IMMUNE SYSTEM / Malaria / Sporozoite / Circumsporozoite protein / Antibody | ||||||
Function / homology | ![]() entry into host cell by a symbiont-containing vacuole / IgG binding / side of membrane / cell surface / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pholcharee, T. / Oyen, D. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum. Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / Richter King, C. / Zavala, F. / Wilson, I.A. #1: ![]() Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / King, C.R. / Zavala, F. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.5 KB | Display | ![]() |
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PDB format | ![]() | 155.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437 KB | Display | ![]() |
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Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w05C ![]() 6wfwC ![]() 6wfxC ![]() 6wfyC ![]() 6wfzC ![]() 6wg0C ![]() 6wg1C ![]() 6wg2C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 6327.939 Da / Num. of mol.: 1 / Fragment: domain III (UNP residues 438-497) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23614.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 24197.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein/peptide | Mass: 836.849 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P02893*PLUS |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium chloride, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018 |
Radiation | Monochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 52998 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.951 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2623 / CC1/2: 0.725 / Rpim(I) all: 0.303 / Rsym value: 0.933 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Homology model Resolution: 1.853→48.946 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.76 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.853→48.946 Å
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Refine LS restraints |
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LS refinement shell |
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