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Yorodumi- PDB-6fzl: Crystal structure of human transthyretin double mutant K35T/T119M -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fzl | ||||||
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Title | Crystal structure of human transthyretin double mutant K35T/T119M | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloid / Gatekeeper / Aggregation / 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 / MOLECULAR REPLACEMENT / Resolution: 1.446 Å | ||||||
Authors | Esperante, S. / Ventura, S. / Reverter, D. / Varejao, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation. Authors: Esperante, S.A. / Varejao, N. / Pinheiro, F. / Sant'Anna, R. / Luque-Ortega, J.R. / Alfonso, C. / Sora, V. / Papaleo, E. / Rivas, G. / Reverter, D. / Ventura, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fzl.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fzl.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 6fzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fzl_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 6fzl_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 6fzl_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 6fzl_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/6fzl ftp://data.pdbj.org/pub/pdb/validation_reports/fz/6fzl | HTTPS FTP |
-Related structure data
Related structure data | 6fwdC 6fxuC 1f41S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13779.377 Da / Num. of mol.: 2 / Mutation: K35T, 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: 2.1 Å3/Da / Density % sol: 41.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 7% glycerol, 1.3 M sodium citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.446→63.58 Å / Num. obs: 41465 / % possible obs: 96.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 19.7 / Num. measured all: 267716 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F41 Resolution: 1.446→42.979 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.84
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 46.704 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.31 Å2 / Biso mean: 24.52 Å2 / Biso min: 10.87 Å2
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Refinement step | Cycle: final / Resolution: 1.446→42.979 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: -22.6552 Å / Origin y: -15.7818 Å / Origin z: -13.0577 Å
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Refinement TLS group |
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