+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ln9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the fibril-specific B10 antibody fragment | ||||||
![]() | Immunoglobulin heavy chain antibody variable domain B10 | ||||||
![]() | IMMUNE SYSTEM / Complementarity Determining Regions / CDR / Camelids / Immunoglobulin Heavy Chains / fibril-specific / fibril recognition / Alzheimer's disease / Amyloid | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Parthier, C. / Morgado, I. / Stubbs, M.T. / Faendrich, M. | ||||||
![]() | ![]() Title: Amyloid Fibril Recognition with the Conformational B10 Antibody Fragment Depends on Electrostatic Interactions. Authors: Haupt, C. / Morgado, I. / Kumar, S.T. / Parthier, C. / Bereza, M. / Hortschansky, P. / Stubbs, M.T. / Horn, U. / Fandrich, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 45.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 30.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1ol0S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Antibody | Mass: 15750.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein was selected by phage display from a fully synthetic library that was partly based on naturally occurring sequences from Camelidae Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-FLC / | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Sequence details | THE RESIDUES (-3)-0 ASP TYR LYS ASP ARE N-TERMINAL FLAG TAGS AND RESIDUES HIS 130-135 ARE C-TERMINAL HIS TAGS. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 200mM Sodium Citrate, 2M Ammonium Sulphate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2009 |
Radiation | Monochromator: Double crystal monochromator with 2 sets of mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 19869 / Num. obs: 19838 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.063 / Net I/σ(I): 21.05 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2955 / Rsym value: 0.69 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1OL0 Resolution: 1.8→18.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.935 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.106 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 35.991 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→18.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 11.287 Å / Origin y: -27.963 Å / Origin z: 3.668 Å
|