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- PDB-4wnj: Crystal structure of Transthyretin-quercetin complex -

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Basic information

Entry
Database: PDB / ID: 4wnj
TitleCrystal structure of Transthyretin-quercetin complex
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloidosis / protein misfolding / negative cooperativity / fibrillogenesis inhibitors / transthyretin stabilizers
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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
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
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsZanotti, G. / Cianci, M. / Berni, R. / Folli, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural evidence for asymmetric ligand binding to transthyretin.
Authors: Cianci, M. / Folli, C. / Zonta, F. / Florio, P. / Berni, R. / Zanotti, G.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0135
Polymers27,5552
Non-polymers4593
Water3,693205
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02610
Polymers55,1094
Non-polymers9176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8530 Å2
ΔGint-46 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.858, 85.782, 63.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

21A-394-

HOH

31B-301-

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) / Gene: TTR, PALB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02766
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein (5 mg/ml) in 20 mM sodium phosphate at pH 7. The reservoir solution was 2.0 M ammonium sulfate, 0.1 M KCl, 0.05 M sodium phosphate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.398→42.891 Å / Num. obs: 47208 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 27.3
Reflection shellResolution: 1.398→1.47 Å / Redundancy: 6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1647)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.398→42.891 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 4455 5.01 %Random selection
Rwork0.1557 ---
obs0.1575 47102 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.398→42.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 30 205 2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131892
X-RAY DIFFRACTIONf_angle_d1.4442590
X-RAY DIFFRACTIONf_dihedral_angle_d13.631660
X-RAY DIFFRACTIONf_chiral_restr0.066293
X-RAY DIFFRACTIONf_plane_restr0.012329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3982-1.41410.28841370.23872613X-RAY DIFFRACTION91
1.4141-1.43070.24691500.21772871X-RAY DIFFRACTION100
1.4307-1.44820.2871460.2272817X-RAY DIFFRACTION99
1.4482-1.46650.24281530.20212845X-RAY DIFFRACTION100
1.4665-1.48580.29171520.22552824X-RAY DIFFRACTION99
1.4858-1.50610.26291470.1922840X-RAY DIFFRACTION100
1.5061-1.52770.2361480.19992811X-RAY DIFFRACTION99
1.5277-1.55050.22221510.16862876X-RAY DIFFRACTION100
1.5505-1.57470.20611460.15372824X-RAY DIFFRACTION99
1.5747-1.60050.20191540.13962842X-RAY DIFFRACTION100
1.6005-1.62810.19781520.13972806X-RAY DIFFRACTION100
1.6281-1.65770.18611500.14772819X-RAY DIFFRACTION100
1.6577-1.68960.2521450.14382861X-RAY DIFFRACTION100
1.6896-1.72410.2081560.1422865X-RAY DIFFRACTION100
1.7241-1.76160.18491500.13982830X-RAY DIFFRACTION100
1.7616-1.80260.15611530.13722846X-RAY DIFFRACTION100
1.8026-1.84760.1911510.13112844X-RAY DIFFRACTION100
1.8476-1.89760.1591480.13772826X-RAY DIFFRACTION99
1.8976-1.95340.21491400.17842662X-RAY DIFFRACTION92
1.9534-2.01650.16371490.13552841X-RAY DIFFRACTION100
2.0165-2.08850.19761530.13342812X-RAY DIFFRACTION99
2.0885-2.17220.1441530.13032831X-RAY DIFFRACTION99
2.1722-2.2710.15371320.14672631X-RAY DIFFRACTION92
2.271-2.39070.16131500.14762824X-RAY DIFFRACTION100
2.3907-2.54050.21761460.15372857X-RAY DIFFRACTION100
2.5405-2.73660.18421530.16152827X-RAY DIFFRACTION100
2.7366-3.0120.22951450.17122817X-RAY DIFFRACTION99
3.012-3.44760.19311520.16062851X-RAY DIFFRACTION100
3.4476-4.3430.17761450.14032756X-RAY DIFFRACTION97
4.343-42.91120.18981480.16592842X-RAY DIFFRACTION99

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