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Yorodumi- PDB-3ipe: Human Transthyretin (TTR) complexed with a palindromic bivalent a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ipe | ||||||
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Title | Human Transthyretin (TTR) complexed with a palindromic bivalent amyloid inhibitor (7 carbon linker). | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE / Amyloid / Inhibitor / Palindrome / Amyloidosis / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Neuropathy / Secreted / Thyroid hormone / Transport | ||||||
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: 1.4 Å | ||||||
Authors | Kolstoe, S.E. / Wood, S.P. / Pepys, M.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Trapping of palindromic ligands within native transthyretin prevents amyloid formation. Authors: Kolstoe, S.E. / Mangione, P.P. / Bellotti, V. / Taylor, G.W. / Tennent, G.A. / Deroo, S. / Morrison, A.J. / Cobb, A.J. / Coyne, A. / McCammon, M.G. / Warner, T.D. / Mitchell, J. / Gill, R. / ...Authors: Kolstoe, S.E. / Mangione, P.P. / Bellotti, V. / Taylor, G.W. / Tennent, G.A. / Deroo, S. / Morrison, A.J. / Cobb, A.J. / Coyne, A. / McCammon, M.G. / Warner, T.D. / Mitchell, J. / Gill, R. / Smith, M.D. / Ley, S.V. / Robinson, C.V. / Wood, S.P. / Pepys, M.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ipe.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ipe.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ipe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ipe_validation.pdf.gz | 676.1 KB | Display | wwPDB validaton report |
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Full document | 3ipe_full_validation.pdf.gz | 679.4 KB | Display | |
Data in XML | 3ipe_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3ipe_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/3ipe ftp://data.pdbj.org/pub/pdb/validation_reports/ip/3ipe | HTTPS FTP |
-Related structure data
Related structure data | 3ipbC 3m1oC 2roxS 3ipg C: citing same article (ref.) S: Starting model for refinement |
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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 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766 #2: Chemical | ChemComp-JZE / | #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: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 298 K / pH: 4.5 Details: 25- 32% v/v PEG550-monomethyl ether, 70 mM NaAc buffer pH 4-5 and 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC / Detector: CCD / Date: Sep 29, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43 Å / Num. obs: 45900 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.4→1.48 Å / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ROX Resolution: 1.4→35.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.194 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 16.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→35.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Total num. of bins used: 20
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