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- PDB-4wns: Crystal structure of Transthyretin complexed with pterostilbene -

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Basic information

Entry
Database: PDB / ID: 4wns
TitleCrystal structure of Transthyretin complexed with pterostilbene
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / amyloidosis / negative cooperativity / fibrillogenesis inhibitors
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase 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
Pterostilbene / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsZanotti, G. / Cianci, M. / Folli, C. / Berni, R.
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 14, 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 ...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 / pdbx_struct_special_symmetry
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)28,2388
Polymers27,5552
Non-polymers6836
Water3,297183
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,47516
Polymers55,1094
Non-polymers1,36612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)42.702, 85.583, 64.153
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
11B-204-

3RL

21B-204-

3RL

31A-334-

HOH

41A-351-

HOH

51A-352-

HOH

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-3RL / Pterostilbene / Pterostilbene


Mass: 256.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The protein (5 mg/ml) was in 20 mM sodium phosphate at pH 7. Reservoir solution: 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: 1.399→42.791 Å / Num. obs: 47156 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 36.9
Reflection shellResolution: 1.399→1.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.8 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1647) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNJ

4wnj


Resolution: 1.399→42.79 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 4448 4.99 %Random selection
Rwork0.1676 ---
obs0.1685 47087 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 41 183 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011933
X-RAY DIFFRACTIONf_angle_d1.3142650
X-RAY DIFFRACTIONf_dihedral_angle_d12.683678
X-RAY DIFFRACTIONf_chiral_restr0.077301
X-RAY DIFFRACTIONf_plane_restr0.008340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3992-1.41510.24971410.26222665X-RAY DIFFRACTION94
1.4151-1.43180.27561440.25822830X-RAY DIFFRACTION100
1.4318-1.44920.28551530.25652830X-RAY DIFFRACTION100
1.4492-1.46760.28291460.24912829X-RAY DIFFRACTION100
1.4676-1.48690.23381480.2292818X-RAY DIFFRACTION99
1.4869-1.50720.23851460.22822848X-RAY DIFFRACTION100
1.5072-1.52880.24051540.23282849X-RAY DIFFRACTION100
1.5288-1.55160.21891480.22162802X-RAY DIFFRACTION100
1.5516-1.57590.21241510.21282862X-RAY DIFFRACTION100
1.5759-1.60170.24361400.19812806X-RAY DIFFRACTION99
1.6017-1.62930.20881520.19242821X-RAY DIFFRACTION100
1.6293-1.65890.19731470.19972814X-RAY DIFFRACTION100
1.6589-1.69080.22361520.1922868X-RAY DIFFRACTION100
1.6908-1.72540.22181430.19212816X-RAY DIFFRACTION100
1.7254-1.76290.23461480.19892809X-RAY DIFFRACTION100
1.7629-1.80390.20561510.19052853X-RAY DIFFRACTION100
1.8039-1.8490.17471520.17612851X-RAY DIFFRACTION100
1.849-1.8990.16541480.16912803X-RAY DIFFRACTION100
1.899-1.95490.17951510.16762873X-RAY DIFFRACTION100
1.9549-2.0180.18871520.16292834X-RAY DIFFRACTION100
2.018-2.09010.2161550.16412797X-RAY DIFFRACTION100
2.0901-2.17380.20321470.15542818X-RAY DIFFRACTION99
2.1738-2.27270.17911420.14832836X-RAY DIFFRACTION99
2.2727-2.39250.17371490.15772830X-RAY DIFFRACTION100
2.3925-2.54240.1641450.15332829X-RAY DIFFRACTION100
2.5424-2.73870.20041460.15372869X-RAY DIFFRACTION100
2.7387-3.01420.21520.16162788X-RAY DIFFRACTION100
3.0142-3.45020.18051510.15082827X-RAY DIFFRACTION100
3.4502-4.34620.14711490.13772802X-RAY DIFFRACTION98
4.3462-42.81150.15421450.16622825X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.4242 Å / Origin y: 29.9119 Å / Origin z: 47.9005 Å
111213212223313233
T0.1098 Å2-0.0002 Å2-0.0255 Å2-0.1075 Å20.0029 Å2--0.1256 Å2
L0.6126 °20.0216 °2-0.3713 °2-0.8359 °2-0.0908 °2--0.577 °2
S-0.0452 Å °-0.0154 Å °-0.1033 Å °0.016 Å °-0.0411 Å °0.0068 Å °-0.0081 Å °0.0176 Å °0.0688 Å °
Refinement TLS groupSelection details: all

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