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Open data
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Basic information
Entry | Database: PDB / ID: 1ie4 | |||||||||
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Title | RAT TRANSTHYRETIN COMPLEX WITH THYROXINE (T4) | |||||||||
![]() | TRANSTHYRETIN | |||||||||
![]() | TRANSPORT PROTEIN / TRANSPORT OF THYROID HORMONES / RAT TRANSTHYRETIN / PREALBUMIN / THYROXINE COMPLEX | |||||||||
Function / homology | ![]() The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wojtczak, A. | |||||||||
![]() | ![]() Title: Structure of rat transthyretin (rTTR) complex with thyroxine at 2.5 A resolution: first non-biased insight into thyroxine binding reveals different hormone orientation in two binding sites. Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W. #1: ![]() Title: Structures of Human Transthyretin Complexed with Thyroxine at 2.0 ? Resolution and 3',5'-Dinitro-N-acetyl-L-thyronine at 2.2 ? Resolution Authors: Wojtczak, A. / Cody, V. / Luft, J. / Pangborn, W. #2: ![]() Title: Crystal Structure of Rat Transthyretin at 2.5 A Resolution: First Report on a Unique Tetrameric Structure. Authors: Wojtczak, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 82.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.3 KB | Display | ![]() |
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Full document | ![]() | 512.3 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gkeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 13614.147 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: THIS SEQUENCE OCCURS NATURALLY IN RAT; PURIFIED FROM NATURAL SOURCE (SERUM) Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.472 Å3/Da / Density % sol: 50.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Ammonium sulfate, acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: Collimator |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→82.5 Å / Num. all: 18890 / Num. obs: 18890 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1786 / % possible all: 82.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 82.5 Å / Num. obs: 16558 / % possible obs: 83.5 % / Num. measured all: 83761 |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GKE Resolution: 2.5→12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 177534.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.32 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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