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Open data
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Basic information
Entry | Database: PDB / ID: 3djz | ||||||
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Title | Crystal structure of transthyretin variant L55P at neutral pH | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / TTR / AMYLOID FIBRILS / POINT MUTATION / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Cendron, L. / Zanotti, G. / Folli, C. / Berni, R. | ||||||
![]() | ![]() Title: Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses. Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / Berni, R. #1: ![]() Title: Acidic Ph-Induced Conformational Changes in Amyloidogenic Mutant Transthyretin. Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G. #2: ![]() Title: A Comparative Analysis of 23 Structures of the Amyloidogenic Protein Transthyretin. Authors: Eneqvist, T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.6 KB | Display | ![]() |
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PDB format | ![]() | 46.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
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Full document | ![]() | 443.5 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3djrC ![]() 3djsC ![]() 3djtC ![]() 3dk0C ![]() 3dk2C ![]() 1f41S S: Starting model for refinement C: citing same article ( |
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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: 13761.317 Da / Num. of mol.: 2 / Mutation: L55P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: 32% PEG 400, 0.05-0.2M CaCl2, 0.1M NaHepes , pH 7.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9859 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→66.67 Å / Num. all: 21935 / Num. obs: 21935 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.82→1.92 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3157 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F41 Resolution: 1.82→66.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.639 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→66.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Total num. of bins used: 20
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