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- PDB-6wfx: Crystal structure of Fab395 in complex with NPNA2 peptide from ci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wfx | ||||||
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Title | Crystal structure of Fab395 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 / side of membrane / cell surface / 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 | ![]() | 177.6 KB | Display | ![]() |
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PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6w00C ![]() 6w05C ![]() 6wfwC ![]() 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: 24283.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23475.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 834.857 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P02893*PLUS |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 30% PEG4000, 0.2 M ammonium acetate, 0.1 M sodium citrate, pH 5.6 |
-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: Mar 29, 2019 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03324 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 16577 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.787 / Rpim(I) all: 0.114 / Rsym value: 0.276 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 749 / CC1/2: 0.338 / Rpim(I) all: 0.77 / Rsym value: 1.762 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Homology model Resolution: 2.59→47.917 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / 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: 2.59→47.917 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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