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- PDB-6sug: Crystal structure of transthyretin in complex with 3-deoxytolcapo... -

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Basic information

Entry
Database: PDB / ID: 6sug
TitleCrystal structure of transthyretin in complex with 3-deoxytolcapone, a tolcapone analogue
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis / tetramer / binding protein
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
3-deoxytolcapone / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsLoconte, V. / Cianci, M. / Menozzi, I. / Sbravati, D. / Sansone, F. / Casnati, A. / Berni, R.
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Interactions of tolcapone analogues as stabilizers of the amyloidogenic protein transthyretin.
Authors: Loconte, V. / Cianci, M. / Menozzi, I. / Sbravati, D. / Sansone, F. / Casnati, A. / Berni, R.
History
DepositionSep 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: 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 24, 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)32,3244
Polymers31,8102
Non-polymers5142
Water3,621201
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6498
Polymers63,6204
Non-polymers1,0294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6770 Å2
ΔGint-40 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.012, 85.559, 64.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

LVB

21A-201-

LVB

31A-201-

LVB

41B-201-

LVB

51B-201-

LVB

61B-201-

LVB

71B-201-

LVB

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Components

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


Mass: 15904.984 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 (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-LVB / 3-deoxytolcapone


Mass: 257.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.99 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2 M ammonium sulfate, 0.1M KCl, 30 mM sodium phosphate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.21→64.529 Å / Num. obs: 72459 / % possible obs: 98.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.03 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.026 / Rsym value: 0.055 / Net I/σ(I): 15.6
Reflection shellResolution: 1.21→1.23 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3396 / CC1/2: 0.518 / Rpim(I) all: 0.54 / Rsym value: 1.031

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AKS

5aks


Resolution: 1.21→35.79 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 3536 4.88 %RANDOM
Rwork0.147 68869 --
obs0.1481 72405 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.29 Å2 / Biso mean: 22.2755 Å2 / Biso min: 9.48 Å2
Refinement stepCycle: final / Resolution: 1.21→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 58 201 2044
Biso mean--35.33 31.46 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.21-1.22660.27531420.2533260594
1.2266-1.24410.25791270.2227269498
1.2441-1.26270.24151480.2109268798
1.2627-1.28240.24921320.1873270198
1.2824-1.30340.2131590.18265597
1.3034-1.32590.22531510.1788270598
1.3259-1.350.1911490.1616269597
1.35-1.3760.19811570.1489272499
1.376-1.40410.18331480.142268498
1.4041-1.43460.16971450.1335275299
1.4346-1.4680.14971360.1229271399
1.468-1.50470.14381450.1187274699
1.5047-1.54540.17381280.11852798100
1.5454-1.59090.1291180.11342779100
1.5909-1.64220.14611340.1113274498
1.6422-1.70090.14381600.1171274299
1.7009-1.7690.15871390.1201274199
1.769-1.84950.14311270.1223277199
1.8495-1.9470.14831360.12132815100
1.947-2.0690.1311300.12272799100
2.069-2.22870.1561680.12832790100
2.2287-2.45290.15971220.14292829100
2.4529-2.80780.17251500.1611282699
2.8078-3.5370.1921320.1621287099
3.537-35.790.17981530.16813004100

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