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Open data
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Basic information
Entry | Database: PDB / ID: 4abq | ||||||
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Title | CRYSTAL STRUCTURE OF TRANSTHYRETIN IN COMPLEX WITH LIGAND C-1 | ||||||
![]() | TRANSTHYRETIN | ||||||
![]() | TRANSPORT PROTEIN | ||||||
Function / homology | ![]() Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tomar, D. / Khan, T. / Singh, R.R. / Mishra, S. / Gupta, S. / Surolia, A. / Salunke, D.M. | ||||||
![]() | ![]() Title: Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites. Authors: Tomar, D. / Khan, T. / Singh, R.R. / Mishra, S. / Gupta, S. / Surolia, A. / Salunke, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.2 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4abuC ![]() 4abvC ![]() 4abwC ![]() 4ac2C ![]() 4ac4C ![]() 4ankC ![]() 1dvqS C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 13421.952 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.5 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: POTASSIUM CHLORIDE, POTASSIUM PHOSPHATE, AMMONIUM SULFATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 6, 2009 / Details: BENT COLLIMATING MIRROR AND TOROID |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.6 Å / Num. obs: 26484 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.7→5.3 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.5 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DVQ Resolution: 1.7→63.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.257 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.026 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→63.93 Å
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Refine LS restraints |
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