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- PDB-7qc5: Crystal structure of human wild type transthyretin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7qc5
TitleCrystal structure of human wild type transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone compound
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine (T4) binding site / stabilization compound / amyloid fibrils.
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
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
Similarity search - Domain/homology
Chem-AQI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsVarejao, N. / Pinheiro, F. / Pallares, I. / Ventura, S. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098423-B-I00 Spain
CitationJournal: J.Med.Chem. / Year: 2022
Title: Development of a Highly Potent Transthyretin Amyloidogenesis Inhibitor: Design, Synthesis, and Evaluation.
Authors: Pinheiro, F. / Pallares, I. / Peccati, F. / Sanchez-Morales, A. / Varejao, N. / Bezerra, F. / Ortega-Alarcon, D. / Gonzalez, D. / Osorio, M. / Navarro, S. / Velazquez-Campoy, A. / Almeida, M. ...Authors: Pinheiro, F. / Pallares, I. / Peccati, F. / Sanchez-Morales, A. / Varejao, N. / Bezerra, F. / Ortega-Alarcon, D. / Gonzalez, D. / Osorio, M. / Navarro, S. / Velazquez-Campoy, A. / Almeida, M.R. / Reverter, D. / Busque, F. / Alibes, R. / Sodupe, M. / Ventura, S.
History
DepositionNov 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,1414
Polymers27,5552
Non-polymers5862
Water4,252236
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2828
Polymers55,1094
Non-polymers1,1734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)84.374, 43.818, 65.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-201-

AQI

21A-201-

AQI

31B-201-

AQI

41B-201-

AQI

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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
Details: Wild type TTR / Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-AQI / (3-fluoranyl-5-oxidanyl-phenyl)-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone / (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone


Mass: 293.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8FNO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400, hepes, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.2→43.82 Å / Num. obs: 76526 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.018 / Rrim(I) all: 0.042 / Net I/σ(I): 17.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3745 / CC1/2: 0.83 / Rpim(I) all: 0.308 / Rrim(I) all: 0.726 / Χ2: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASER1.19.2_4158phasing
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.2→38.89 Å / SU ML: 0.0838 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1746 3751 4.91 %
Rwork0.1596 72709 -
obs0.1603 76460 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.22 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 42 245 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221957
X-RAY DIFFRACTIONf_angle_d1.2542687
X-RAY DIFFRACTIONf_chiral_restr0.1125296
X-RAY DIFFRACTIONf_plane_restr0.0111348
X-RAY DIFFRACTIONf_dihedral_angle_d10.1856270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.22891360.22132687X-RAY DIFFRACTION99.96
1.22-1.230.25771280.21342639X-RAY DIFFRACTION100
1.23-1.250.17951200.2012680X-RAY DIFFRACTION99.96
1.25-1.270.17681390.18352667X-RAY DIFFRACTION99.93
1.27-1.280.19211260.17322686X-RAY DIFFRACTION99.82
1.28-1.30.19411300.17752652X-RAY DIFFRACTION99.86
1.3-1.330.16581350.17742671X-RAY DIFFRACTION99.89
1.33-1.350.18921460.16832645X-RAY DIFFRACTION99.96
1.35-1.370.15041700.15372655X-RAY DIFFRACTION100
1.37-1.40.15761290.15352673X-RAY DIFFRACTION99.93
1.4-1.430.18161580.15692649X-RAY DIFFRACTION100
1.43-1.460.17991540.1492689X-RAY DIFFRACTION99.96
1.46-1.490.15331330.15282644X-RAY DIFFRACTION99.93
1.49-1.530.16541380.14612684X-RAY DIFFRACTION100
1.53-1.570.1691280.13652714X-RAY DIFFRACTION99.93
1.57-1.620.13521420.1352676X-RAY DIFFRACTION99.96
1.62-1.670.14431390.13622687X-RAY DIFFRACTION100
1.67-1.730.1441280.14622698X-RAY DIFFRACTION99.89
1.73-1.80.16741540.1532670X-RAY DIFFRACTION100
1.8-1.880.15271380.15632718X-RAY DIFFRACTION99.9
1.88-1.980.16331320.14822711X-RAY DIFFRACTION99.89
1.98-2.110.17221160.14942736X-RAY DIFFRACTION99.89
2.11-2.270.17591440.14672713X-RAY DIFFRACTION99.86
2.27-2.50.16471450.16062705X-RAY DIFFRACTION99.75
2.5-2.860.20091440.17422736X-RAY DIFFRACTION99.28
2.86-3.60.15531490.16362763X-RAY DIFFRACTION99.08
3.6-38.890.20231500.16472861X-RAY DIFFRACTION97.86

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