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- PDB-6tjn: Human transthyretin (TTR) complexed with (E)-3-(((4-hydroxybenzyl... -

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Basic information

Entry
Database: PDB / ID: 6tjn
TitleHuman transthyretin (TTR) complexed with (E)-3-(((4-hydroxybenzylidene)amino)oxy)propanoic acid
ComponentsTransthyretin
KeywordsPROTEIN TRANSPORT / Transthyretin / TTR / inhibitor / complex
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-NEK / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsCiccone, L. / Shepard, W. / Nencetti, S. / Orlandini, E. / Rossello, A.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Monoaryl derivatives as transthyretin fibril formation inhibitors: Design, synthesis, biological evaluation and structural analysis.
Authors: Ciccone, L. / Nencetti, S. / Tonali, N. / Fruchart-Gaillard, C. / Shepard, W. / Nuti, E. / Camodeca, C. / Rossello, A. / Orlandini, E.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0874
Polymers27,6692
Non-polymers4182
Water3,711206
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1748
Polymers55,3384
Non-polymers8374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6870 Å2
ΔGint-47 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.190, 85.870, 63.940
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-

NEK

21A-201-

NEK

31A-343-

HOH

41B-362-

HOH

51B-390-

HOH

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Components

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


Mass: 13834.413 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-NEK / 3-[(~{E})-(4-hydroxyphenyl)methylideneamino]oxypropanoic acid


Mass: 209.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein: 4.93 mg/mL, Tris pH 8.0, 150mM NaCl. Reservoir: 24% PEG 600, 0.2 Imidazole Malate pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2019
RadiationMonochromator: Cryogenically cooled channel cut Si[111] crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26756 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.99 / Net I/σ(I): 14.62
Reflection shellResolution: 1.71→1.72 Å / Num. unique obs: 52925 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQ8

4tq8


Resolution: 1.702→38.584 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.1925 1337 5 %
Rwork0.1744 --
obs0.1753 26749 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.28 Å2 / Biso mean: 38.5857 Å2 / Biso min: 15.91 Å2
Refinement stepCycle: final / Resolution: 1.702→38.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 50 206 2052
Biso mean--90.84 49.16 -
Num. residues----232
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.702-1.76280.41981290.3984246398
1.7628-1.83340.32011320.33312498100
1.8334-1.91680.30511310.25042499100
1.9168-2.01790.24691320.19562504100
2.0179-2.14430.21961350.18212551100
2.1443-2.30980.21561310.16162500100
2.3098-2.54220.22181350.16162554100
2.5422-2.910.14721340.15642551100
2.91-3.66580.16941350.15552575100
Refinement TLS params.Method: refined / Origin x: 1.1722 Å / Origin y: 12.9763 Å / Origin z: 15.5906 Å
111213212223313233
T0.1868 Å2-0.0158 Å2-0.0039 Å2-0.1641 Å2-0.0087 Å2--0.2095 Å2
L1.292 °20.0237 °20.3076 °2-1.1854 °20.0568 °2--1.6649 °2
S-0.0022 Å °-0.0746 Å °0.1827 Å °0.0951 Å °-0.053 Å °-0.0021 Å °-0.0547 Å °-0.0749 Å °0.0552 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 201
2X-RAY DIFFRACTION1allB9 - 201
3X-RAY DIFFRACTION1allS1 - 218

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