+Open data
-Basic information
Entry | Database: PDB / ID: 7sbz | ||||||
---|---|---|---|---|---|---|---|
Title | JAR5 Fab bound to fHbp v1.1 crystallized in space group I422 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Complex | ||||||
Function / homology | Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / : / Factor H binding protein Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Neisseria meningitidis serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Chesterman, C. / Malito, E. / Bottomley, M.J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Active Learning for Rapid Design: An iterative AI approach for accelerated vaccine design that combines active machine learning and high-throughput experimental evaluation Authors: Chesterman, C. / Desautels, T. / Sierra, L.J. / Arrildt, K. / Zemla, A. / Lau, E.Y. / Sundaram, S. / Laliberte, J. / Chen, L. / Ruby, A. / Mednikov, M. / Bertholet, S. / Yu, D. / Luisi, K. / ...Authors: Chesterman, C. / Desautels, T. / Sierra, L.J. / Arrildt, K. / Zemla, A. / Lau, E.Y. / Sundaram, S. / Laliberte, J. / Chen, L. / Ruby, A. / Mednikov, M. / Bertholet, S. / Yu, D. / Luisi, K. / Malito, E. / Mallet, C. / Bottomley, M.J. / van den Berg, R.A. / Faissol, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7sbz.cif.gz | 268.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7sbz.ent.gz | 212.5 KB | Display | PDB format |
PDBx/mmJSON format | 7sbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sbz_validation.pdf.gz | 484.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7sbz_full_validation.pdf.gz | 508.6 KB | Display | |
Data in XML | 7sbz_validation.xml.gz | 47 KB | Display | |
Data in CIF | 7sbz_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/7sbz ftp://data.pdbj.org/pub/pdb/validation_reports/sb/7sbz | HTTPS FTP |
-Related structure data
Related structure data | 7sa6C 5t5fS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 27566.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23865.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #3: Protein | Mass: 27699.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: E6MV22 #4: Chemical | ChemComp-CD / Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Cadmium Chloride 0.1 M Sodium Acetate pH 4.6 30% PEG 300 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.27 Å / Num. obs: 49617 / % possible obs: 96.83 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.5835 / Rrim(I) all: 0.6071 / Net I/σ(I): 9.48 |
Reflection shell | Resolution: 2.9→3.004 Å / Rmerge(I) obs: 4.16 / Num. unique obs: 4851 / CC1/2: 0.649 / Rrim(I) all: 4.318 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T5F Resolution: 2.9→49.27 Å / SU ML: 0.49 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 33.69 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.27 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|