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- PDB-5al8: Transthyretin binding heterogeneity and anti-amyloidogenic activi... -

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Basic information

Entry
Database: PDB / ID: 5al8
TitleTransthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: daidzein-7-O- glucuronide
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / AMYLOID / FIBRILLOGENESIS / FIBRILLOGENESIS INHIBITORS / POLYPHENOLS / POLYPHENOL METABOLITES / NEGATIVE COOPERATIVITY
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DAIDZEIN-7-O-GLUCURONIDE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFlorio, P. / Foll, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Transthyretin Binding Heterogeneity and Anti-Amyloidogenic Activity of Natural Polyphenols and Their Metabolites
Authors: Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R.
History
DepositionMar 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 15, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / Item: _exptl_crystal_grow.method
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4154
Polymers27,5552
Non-polymers8612
Water4,197233
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8318
Polymers55,1094
Non-polymers1,7214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.062, 84.879, 63.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1126-

D75

21A-1126-

D75

31B-1125-

D75

41B-1125-

D75

51B-1125-

D75

61B-2031-

HOH

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Components

#1: Protein TRANSTHYRETIN / ATTR / PREALBUMIN / TBPA


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) / Plasmid: PET11B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-D75 / DAIDZEIN-7-O-GLUCURONIDE


Mass: 430.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN ...Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013 / Details: KB MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.5→84.88 Å / Num. obs: 37976 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 19.67 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 17.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F41

1f41


Resolution: 1.5→63.549 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1896 5 %
Rwork0.1687 --
obs0.1702 37929 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→63.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 62 233 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122118
X-RAY DIFFRACTIONf_angle_d1.5082924
X-RAY DIFFRACTIONf_dihedral_angle_d14.555756
X-RAY DIFFRACTIONf_chiral_restr0.055327
X-RAY DIFFRACTIONf_plane_restr0.008379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.31721300.25372563X-RAY DIFFRACTION100
1.5375-1.57910.28551380.23452491X-RAY DIFFRACTION99
1.5791-1.62560.25051140.21212566X-RAY DIFFRACTION100
1.6256-1.6780.24591350.21632527X-RAY DIFFRACTION99
1.678-1.7380.21531320.20132564X-RAY DIFFRACTION100
1.738-1.80760.21691120.18982550X-RAY DIFFRACTION100
1.8076-1.88990.19241400.18242563X-RAY DIFFRACTION100
1.8899-1.98950.19811130.17162572X-RAY DIFFRACTION100
1.9895-2.11420.21081460.16742567X-RAY DIFFRACTION100
2.1142-2.27740.18531580.16032549X-RAY DIFFRACTION100
2.2774-2.50660.17921240.16742585X-RAY DIFFRACTION100
2.5066-2.86930.20151400.16592604X-RAY DIFFRACTION99
2.8693-3.6150.20231520.15672603X-RAY DIFFRACTION99
3.615-63.60610.17781620.1542729X-RAY DIFFRACTION99

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