+Open data
-Basic information
Entry | Database: PDB / ID: 3tct | ||||||
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Title | Structure of wild-type TTR in complex with tafamidis | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE / BINDING PROTEIN / AMYLOID / AMYLOIDOSIS / DISEASE MUTATION / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / NEUROPATHY / SECRETED / THYROID HORMONE / TRANSPORT / Kinetic Stabilizer / Inhibition of the Amyloid Cascade | ||||||
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: 1.3 Å | ||||||
Authors | Connelly, S. / Kelly, J.W. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Tafamidis, a potent and selective transthyretin kinetic stabilizer that inhibits the amyloid cascade. Authors: Bulawa, C.E. / Connelly, S. / Devit, M. / Wang, L. / Weigel, C. / Fleming, J.A. / Packman, J. / Powers, E.T. / Wiseman, R.L. / Foss, T.R. / Wilson, I.A. / Kelly, J.W. / Labaudiniere, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tct.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tct.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 3tct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/3tct ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tct | HTTPS FTP |
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-Related structure data
Related structure data | 2fbrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: unp residues 21-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: PMMHA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): EPICUREAN GOLD / References: UniProt: P02766 #2: Chemical | #3: 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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | pH: 5.5 Details: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS ...Details: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS WERE GROWN FROM 1.395 M SODIUM CITRATE, 3.5% V/V GLYCEROL AT PH 5.5. THE CRYSTALS WERE FROZEN USING A CRYO-PROTECTANT SOLUTION OF 1.395 M SODIUM CITRATE, PH 5.5, CONTAINING 10% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 / Wavelength: 0.9795 Å | ||||||||||||||||||
Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.3→50 Å / Num. obs: 58308 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 51.5 | ||||||||||||||||||
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FBR Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.383 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 20.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.33 Å / Total num. of bins used: 20
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