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- PDB-6suh: Crystal structure of human transthyretin in complex with 3-O-meth... -

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Basic information

Entry
Database: PDB / ID: 6suh
TitleCrystal structure of human transthyretin in complex with 3-O-methyltolcapone, a tolcapone analogue
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis / tetramer / binding protein
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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, 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-O-methyltolcapone / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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)32,3854
Polymers31,8102
Non-polymers5752
Water3,423190
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7698
Polymers63,6204
Non-polymers1,1494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)42.912, 85.462, 64.708
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
11B-201-

LVE

21A-356-

HOH

31B-334-

HOH

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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-LVE / 3-O-methyltolcapone


Mass: 287.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.88 Å3/Da / Density % sol: 33.89 %
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: 1.26→42.91 Å / Num. obs: 64681 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 11 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.058 / Rsym value: 0.086 / Net I/σ(I): 11.1
Reflection shellResolution: 1.26→1.28 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3086 / CC1/2: 0.485 / Rpim(I) all: 0.96 / Rsym value: 1.44

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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: 1.26→42.731 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 3250 5.04 %RANDOM
Rwork0.1549 61260 --
obs0.1561 64510 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.38 Å2 / Biso mean: 21.3909 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: final / Resolution: 1.26→42.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 68 190 2043
Biso mean--18.77 29.96 -
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 (%)
1.26-1.27880.25851200.2317256997
1.2788-1.29880.24931520.2089262699
1.2988-1.32010.20821350.1896258298
1.3201-1.34290.19471320.1807265499
1.3429-1.36730.21461320.1745256799
1.3673-1.39360.20011430.171263499
1.3936-1.4220.19441430.1671263099
1.422-1.45290.18751340.1581263899
1.4529-1.48670.22531330.1538264799
1.4867-1.52390.19581380.1396264299
1.5239-1.56510.14441370.1338264499
1.5651-1.61120.16141470.12982649100
1.6112-1.66320.16631640.133263799
1.6632-1.72260.17211260.1395269799
1.7226-1.79160.16861380.1382664100
1.7916-1.87320.17431440.13162665100
1.8732-1.97190.14581370.13122676100
1.9719-2.09540.14941390.13472704100
2.0954-2.25720.16291380.13482706100
2.2572-2.48440.17551530.14772692100
2.4844-2.84380.1741610.1637271899
2.8438-3.58260.19461520.16572753100
3.5826-42.7310.18391520.1725286699

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