+Open data
-Basic information
Entry | Database: PDB / ID: 1fhn | ||||||
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Title | TRANSTHYRETIN STABILITY AS A KEY FACTOR IN AMYLOIDOGENESIS | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloid / Transthyretin / Protein Stability | ||||||
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 / Resolution: 1.75 Å | ||||||
Authors | Sebastiao, M.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Transthyretin stability as a key factor in amyloidogenesis: X-ray analysis at atomic resolution. Authors: Sebastiao, M.P. / Lamzin, V. / Saraiva, M.J. / Damas, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fhn.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fhn.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fhn_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 1fhn_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 1fhn_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1fhn_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/1fhn ftp://data.pdbj.org/pub/pdb/validation_reports/fh/1fhn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the biological assembly is a homotetramer constructed from chains A and B and a symmetry partner generated by crystallographic two-fold symmetry. |
-Components
#1: Protein | Mass: 13807.452 Da / Num. of mol.: 2 / Mutation: T119M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.73 % | ||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: Ammonium Sulphate, Citrate Buffer, Glycerol, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 287K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 5.3 / Method: vapor diffusion, hanging drop / Details: Damas, A.M., (1996) Acta Crystallog., D52, 966. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→12 Å / Num. all: 101000 / Num. obs: 100492 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.45 / Num. unique all: 25123 / % possible all: 99.3 |
Reflection | *PLUS Num. obs: 25047 / Num. measured all: 101000 |
-Processing
Software |
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Refinement | Resolution: 1.75→8 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→8 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 4 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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