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- PDB-2try: TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2try | ||||||
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Title | TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS AND IMPLICATIONS FOR AMYLOID FIBRIL FORMATION | ||||||
![]() | TRANSTHYRETIN | ||||||
![]() | TRANSPORT / ALBUMIN / RETINOL-BINDING / VITAMIN A / AMYLOID / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / THYROXINE / PREALBUMIN | ||||||
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 | ![]() ![]() | ||||||
![]() | Schormann, N. / Murrell, J.R. / Benson, M.D. | ||||||
![]() | ![]() Title: Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation. Authors: Schormann, N. / Murrell, J.R. / Benson, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.6 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.6 KB | Display | ![]() |
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Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b0wC ![]() 1bzdC ![]() 1bzeC ![]() 1tshC ![]() 2trhC ![]() 1ttaS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99044, 0.13681, -0.01781), Vector: |
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Components
#1: Protein | Mass: 13853.457 Da / Num. of mol.: 2 / Mutation: VARIANT S77Y 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: 2.2 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | pH: 6.5 Details: PURIFIED PROTEIN (25MG/ML IN 100MM TRIS BUFFER, PH 7.5) WAS CRYSTALLIZED FROM 1.5M AMMONIUM SULFATE, 100MM CITRATE BUFFER, PH 5.5, AT ROOM TEMPERATURE., pH 6.5 PH range: 5.5-7.5 / Temp details: room temp |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→64.9 Å / Num. obs: 17581 / % possible obs: 74.9 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.091 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.22 / % possible all: 56 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TTA Resolution: 2→5 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 515.8 / Data cutoff low absF: 7 / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES IN REGIONS WITH LOW ELECTRON DENSITY (RESIDUES 1 - 9 AT N-TERMINUS AND RESIDUES 124 - 127 AT C-TERMINUS) WERE REFINED WITH OCCUPANCIES SET TO 0.5.
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Displacement parameters | Biso mean: 19.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 8
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Xplor file |
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