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Open data
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Basic information
Entry | Database: PDB / ID: 5ttr | ||||||
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Title | LEU 55 PRO TRANSTHYRETIN CRYSTAL STRUCTURE | ||||||
![]() | TRANSTHYRETIN | ||||||
![]() | TRANSPORT / TRANSTHYRETIN / AMYLOID / FAP / THYROXINE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Sebastiao, M.P. / Saraiva, M.J. / Damas, A.M. | ||||||
![]() | ![]() Title: The crystal structure of amyloidogenic Leu55 --> Pro transthyretin variant reveals a possible pathway for transthyretin polymerization into amyloid fibrils. Authors: Sebastiao, M.P. / Saraiva, M.J. / Damas, A.M. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Leu55Pro Variant Transthyretin Authors: Sebastiao, P. / Dauter, Z. / Saraiva, M.J. / Damas, A.M. #2: ![]() Title: Transthyretin Mutation Leu-55-Pro Significantly Alters Tetramer Stability and Increases Amyloidogenicity Authors: Mccutchen, S.L. / Colon, W. / Kelly, J.W. #3: ![]() Title: Transthyretin Pro55, a Variant Associated with Early-Onset, Aggressive, Diffuse Amyloidosis with Cardiac and Neurologic Involvement Authors: Jacobson, D.R. / Mcfarlin, D.E. / Kane, I. / Buxbaum, J.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189 KB | Display | ![]() |
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PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.3 KB | Display | ![]() |
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Full document | ![]() | 546.2 KB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ttaS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.597904, -0.003015, -0.801562), Vector: |
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Components
#1: Protein | Mass: 13761.317 Da / Num. of mol.: 8 / Mutation: L55P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop contained 50:50 mixture of protein and reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.064 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15 Å / Num. obs: 31394 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1 |
Reflection shell | *PLUS % possible obs: 98.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TTA Resolution: 2.7→8 Å / σ(F): 1
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |