+
Open data
-
Basic information
Entry | Database: PDB / ID: 7kjj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Reconstructed ancestor of HIUases and Transthyretins | |||||||||
![]() | TTR ancestor | |||||||||
![]() | TRANSPORT PROTEIN / HORMONE TRANSPORT | |||||||||
Function / homology | 3,5,3',5'-TETRAIODO-L-THYRONINE![]() | |||||||||
Biological species | unidentified (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nagem, R.A.P. / Bleicher, L. / Costa, M.A.F. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies. Authors: Carrijo de Oliveira, L. / Figueiredo Costa, M.A. / Goncalves Pedersolli, N. / Heleno Batista, F.A. / Migliorini Figueira, A.C. / Salgado Ferreira, R. / Alves Pinto Nagem, R. / Alves Nahum, L. / Bleicher, L. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 121.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 89.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 14486.085 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TTR ancestor is a reconstruction of the node right after duplication, corresponding to the ancestor of all modern transthyretins Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.99 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Condition 1: 2 M lithium sulfate, 5% (v/v) 2-propanol, 0.1 M magnesium sulfate, 0.2 M sodium acetate pH 4.5 Condition 2: 30% (w/v) PEG 1500, 20% (w/v) PEG 400, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→41.34 Å / Num. obs: 55503 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.037 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7752 / CC1/2: 0.868 / Rrim(I) all: 0.703 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→40.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|