[English] 日本語
![](img/lk-miru.gif)
- PDB-5f7l: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5f7l | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with Nanobody Nb-ER14 | ||||||||||||||||||
![]() |
| ||||||||||||||||||
![]() | CELL ADHESION / Adhesin / Lectin / Nanobody / Complex | ||||||||||||||||||
Function / homology | SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Adhesin binding fucosylated histo-blood group antigen![]() | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Moonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H. | ||||||||||||||||||
Funding support | ![]() ![]()
| ||||||||||||||||||
![]() | ![]() Title: Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori. Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / ...Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / Coppens, F. / Lo, A.W. / Ny, T. / Solnick, J.V. / Vandenbussche, G. / Oscarson, S. / Hammarstrom, L. / Arnqvist, A. / Berg, D.E. / Muyldermans, S. / Boren, T. / Remaut, H. | ||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 379.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 321.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 497.4 KB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f7kC ![]() 5f7mC ![]() 5f7nC ![]() 5f7wC ![]() 5f7yC ![]() 5f8qC ![]() 5f8rC ![]() 5f93C ![]() 5f97C ![]() 5f9aC ![]() 5f9dC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
#1: Protein | Mass: 49369.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 14190.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium sulfate, 0.1 M Sodium acetate 4.5, 50 % w/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→47.4 Å / Num. obs: 31163 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.74→2.88 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.7 / % possible all: 95.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.74→47.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|