+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dsz | ||||||
---|---|---|---|---|---|---|---|
Title | Engineered human lipocalin 2 in complex with Y-DTPA | ||||||
![]() | engineered human lipocalin 2 | ||||||
![]() | TRANSPORT PROTEIN / protein design / ligand binding protein / beta barrel / engineered lipocalin / de novo protein / protein binding | ||||||
Function / homology | ![]() siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Eichinger, A. / Skerra, A. | ||||||
![]() | ![]() Title: High-affinity recognition of lanthanide(III) chelate complexes by a reprogrammed human lipocalin 2 Authors: Kim, H.J. / Eichinger, A. / Skerra, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21344.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 22% polyethylene glycol 3350, 0.1M Bistris/HCl, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2→66.979 Å / Num. obs: 26827 / % possible obs: 98.2 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 6.1 / Num. unique all: 3813 / Rsym value: 0.372 / % possible all: 97.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 0.423 / Cor.coef. Fo:Fc: 0.579
|
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Solvent computation | Bsol: 56.905 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 81.5 Å2 / Biso mean: 27.759 Å2 / Biso min: 11.34 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Xplor file |
|