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- PDB-7ket: Factor H enhancing human antibody fragment (Fab) to meningococcal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ket | ||||||
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Title | Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein | ||||||
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![]() | IMMUNE SYSTEM / human / antibody / Fab / meningococcal vaccine / Factor H binding protein / complex | ||||||
Function / homology | : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Factor H binding protein variant B24![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beernink, P.T. / Sands, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site. Authors: Sands, N.A. / Beernink, P.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 426.5 KB | Display | ![]() |
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PDB format | ![]() | 320.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ke1C ![]() 7lcvC ![]() 3kvdS S: Starting model for refinement 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: 23661.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 25093.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 28074.248 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: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, polyethylene glycol 3350, tryptone, sodium azide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 6, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 2→107.11 Å / Num. obs: 46166 / % possible obs: 94.96 % / Redundancy: 2.7 % / Biso Wilson estimate: 45.33 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.071 / Rrim(I) all: 0.123 / Net I/σ(I): 8.02 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.66 / Num. unique obs: 3877 / Rpim(I) all: 1.24 / Rrim(I) all: 2.09 / % possible all: 82.44 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: homology model constructed from human Fab; FHbp ID 1 (3KVD) Resolution: 2→107.11 Å / SU ML: 0.4524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.2514 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: 61.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→107.11 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: -16.2387422764 Å / Origin y: 18.14211792 Å / Origin z: -18.5711456552 Å
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Refinement TLS group | Selection details: all |