+Open data
-Basic information
Entry | Database: PDB / ID: 5ttr | ||||||
---|---|---|---|---|---|---|---|
Title | LEU 55 PRO TRANSTHYRETIN CRYSTAL STRUCTURE | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT / TRANSTHYRETIN / AMYLOID / FAP / THYROXINE | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sebastiao, M.P. / Saraiva, M.J. / Damas, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 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: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Leu55Pro Variant Transthyretin Authors: Sebastiao, P. / Dauter, Z. / Saraiva, M.J. / Damas, A.M. #2: Journal: Biochemistry / Year: 1993 Title: Transthyretin Mutation Leu-55-Pro Significantly Alters Tetramer Stability and Increases Amyloidogenicity Authors: Mccutchen, S.L. / Colon, W. / Kelly, J.W. #3: Journal: Hum.Genet. / Year: 1992 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ttr.cif.gz | 189 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ttr.ent.gz | 148.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ttr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/5ttr ftp://data.pdbj.org/pub/pdb/validation_reports/tt/5ttr | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ttaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.597904, -0.003015, -0.801562), Vector: |
-Components
#1: Protein | Mass: 13761.317 Da / Num. of mol.: 8 / Mutation: L55P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.064 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TTA Resolution: 2.7→8 Å / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |