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- PDB-5jim: Crystal Structure of Human Transthyretin in Complex with Perfluor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jim | |||||||||
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Title | Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (PFOS) | |||||||||
![]() | Transthyretin | |||||||||
![]() | TRANSPORT PROTEIN / thyroxine binding / Perfluoroktansulfonsyra (PFOS)complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Begum, A. / Zhang, J. / Olofsson, A. / Andersson, P. / Sauer-Eriksson, A.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Authors: Zhang, J. / Begum, A. / Brannstrom, K. / Grundstrom, C. / Iakovleva, I. / Olofsson, A. / Sauer-Eriksson, A.E. / Andersson, P.L. #1: ![]() Title: Tetrabromobisphenol A Is an Efficient Stabilizer of the Transthyretin Tetramer. Authors: Iakovleva, I. / Begum, A. / Brannstrom, K. / Wijsekera, A. / Nilsson, L. / Zhang, J. / Andersson, P.L. / Sauer-Eriksson, A.E. / Olofsson, 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 | ![]() | 157.3 KB | Display | ![]() |
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PDB format | ![]() | 126.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jidC ![]() 5jiqC ![]() 5l4fC ![]() 5l4iC ![]() 5l4jC ![]() 5l4mC ![]() 1f41S 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: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. PFOS was added at 5 x molar excess to the protein. The reservoir ...Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. PFOS was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent glycerol at pH 5.5. Drop size 3 plus 3 microliter. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.913 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→40 Å / Num. obs: 64626 / % possible obs: 99.76 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 23.41 |
Reflection shell | Resolution: 1.26→1.3 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.97 / % possible all: 98.83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1f41 Resolution: 1.26→38.511 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→38.511 Å
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Refine LS restraints |
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LS refinement shell |
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