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- PDB-4wo0: Crystal structure of transthyretin in complex with apigenin -

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Basic information

Entry
Database: PDB / ID: 4wo0
TitleCrystal structure of transthyretin in complex with apigenin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloidosis / negative cooperativity
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
Chem-AGI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.339 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 15, 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)28,0954
Polymers27,5552
Non-polymers5402
Water5,206289
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1908
Polymers55,1094
Non-polymers1,0814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8571 Å2
ΔGint-62 kcal/mol
Surface area18992 Å2
Unit cell
Length a, b, c (Å)42.660, 85.739, 63.978
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-201-

AGI

21A-201-

AGI

31B-315-

HOH

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Components

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


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-AGI / 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one / Apigenin / Apigenin


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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. 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: 1.339→42.87 Å / Num. obs: 53610 / % possible obs: 98.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 26.2
Reflection shellResolution: 1.339→1.41 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.8 / % possible all: 94.5

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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: 1.339→42.87 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 4767 4.97 %Random selection
Rwork0.1849 ---
obs0.186 52413 93.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.339→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 40 289 2107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061899
X-RAY DIFFRACTIONf_angle_d1.0792601
X-RAY DIFFRACTIONf_dihedral_angle_d13.401682
X-RAY DIFFRACTIONf_chiral_restr0.04290
X-RAY DIFFRACTIONf_plane_restr0.007330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.339-1.35420.33591370.30932648X-RAY DIFFRACTION82
1.3542-1.37020.45981200.4262356X-RAY DIFFRACTION73
1.3702-1.38690.43031390.35872575X-RAY DIFFRACTION80
1.3869-1.40440.26551690.24923172X-RAY DIFFRACTION99
1.4044-1.42290.27811660.24093249X-RAY DIFFRACTION98
1.4229-1.44240.27921620.29552952X-RAY DIFFRACTION94
1.4424-1.4630.3191540.32322929X-RAY DIFFRACTION91
1.463-1.48490.34791530.30242833X-RAY DIFFRACTION88
1.4849-1.50810.30011650.23383174X-RAY DIFFRACTION97
1.5081-1.53280.29621400.28992654X-RAY DIFFRACTION82
1.5328-1.55920.23931610.21323149X-RAY DIFFRACTION98
1.5592-1.58760.21631670.1813234X-RAY DIFFRACTION99
1.5876-1.61810.19641700.17773207X-RAY DIFFRACTION100
1.6181-1.65110.2341680.183235X-RAY DIFFRACTION100
1.6511-1.6870.22751640.1773186X-RAY DIFFRACTION99
1.687-1.72630.25091620.19853122X-RAY DIFFRACTION96
1.7263-1.76950.23491680.19513207X-RAY DIFFRACTION100
1.7695-1.81730.22731680.18073220X-RAY DIFFRACTION100
1.8173-1.87080.2411660.17713267X-RAY DIFFRACTION100
1.8708-1.93120.23471350.17992679X-RAY DIFFRACTION83
1.9312-2.00020.18321580.16363096X-RAY DIFFRACTION96
2.0002-2.08030.19561490.17442835X-RAY DIFFRACTION88
2.0803-2.17490.15171700.15843202X-RAY DIFFRACTION99
2.1749-2.28960.15961520.16382923X-RAY DIFFRACTION91
2.2896-2.4330.16011690.17353200X-RAY DIFFRACTION99
2.433-2.62090.18681750.1783237X-RAY DIFFRACTION100
2.6209-2.88460.19951650.17593094X-RAY DIFFRACTION95
2.8846-3.30180.19261660.1723205X-RAY DIFFRACTION99
3.3018-4.15940.18891570.15253054X-RAY DIFFRACTION95
4.1594-42.89150.17211720.16193222X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.3805 Å / Origin y: 30.1584 Å / Origin z: 48.0163 Å
111213212223313233
T0.0869 Å20.0005 Å2-0.009 Å2-0.0858 Å20.0015 Å2--0.0946 Å2
L0.366 °20.0285 °2-0.1079 °2-0.4093 °2-0.0065 °2--0.2979 °2
S-0.0379 Å °-0.0073 Å °-0.0703 Å °0.0227 Å °-0.0106 Å °0.0056 Å °-0.0127 Å °0.0388 Å °-0.0477 Å °
Refinement TLS groupSelection details: all

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