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- PDB-4tqh: Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylidenea... -

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Basic information

Entry
Database: PDB / ID: 4tqh
TitleHuman transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)ethanoic acid
ComponentsTransthyretin
KeywordsHORMONE / Transthyretin (TTR) complex / Amyloid antagonist and inhibitor / Fluorenone based inhibitor / dual binding mode
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/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
[(9H-fluoren-9-ylideneamino)oxy]acetic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.511 Å
AuthorsCiccone, L. / Nencetti, S. / Rossello, A. / Orlandini, E. / Stura, E.A.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2015
Title: X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors.
Authors: Ciccone, L. / Nencetti, S. / Rossello, A. / Tepshi, L. / Stura, E.A. / Orlandini, E.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.4Sep 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1235
Polymers27,5552
Non-polymers5693
Water5,801322
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,24710
Polymers55,1094
Non-polymers1,1376
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.440, 85.960, 63.000
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-338-

HOH

21B-324-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P02766
#2: Chemical ChemComp-ES8 / [(9H-fluoren-9-ylideneamino)oxy]acetic acid


Mass: 253.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: protein: 5 mg/ml 0.05 M NaCl, 0.05 M Na acetate, pH 5.5 with 1 milli-M ligand. Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 40% (24% MPEG-5K, 0.1M sodium acetate, pH 5.5) ...Details: protein: 5 mg/ml 0.05 M NaCl, 0.05 M Na acetate, pH 5.5 with 1 milli-M ligand. Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 40% (24% MPEG-5K, 0.1M sodium acetate, pH 5.5). Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 12.5% MPEG 5K, 25% MPEG 550, 100 mM (sodium propionate, sodium cacodylate, Bis-Tris-propane(50% component A pH 4; 50% B pH 9.5) and 1 mM ligand.
PH range: 5.5 - 7.0 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87006 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2014
RadiationMonochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87006 Å / Relative weight: 1
ReflectionResolution: 1.51→43 Å / Num. all: 36880 / Num. obs: 36840 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.13 % / Rmerge(I) obs: 0.122 / Rsym value: 0.121 / Net I/σ(I): 12.8
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 9.34 % / Mean I/σ(I) obs: 0.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
Cootmodel building
XDSdata scaling
MxCuBEdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4TQ8

4tq8


Resolution: 1.511→38.055 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1841 5 %Random
Rwork0.1853 ---
obs0.1872 36829 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.511→38.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 42 322 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072617
X-RAY DIFFRACTIONf_angle_d1.6393636
X-RAY DIFFRACTIONf_dihedral_angle_d15.623982
X-RAY DIFFRACTIONf_chiral_restr0.049373
X-RAY DIFFRACTIONf_plane_restr0.006493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.511-1.55180.43791380.43422642X-RAY DIFFRACTION99
1.5518-1.59750.40041370.38042610X-RAY DIFFRACTION100
1.5975-1.6490.33741400.33672663X-RAY DIFFRACTION100
1.649-1.7080.34841410.32482662X-RAY DIFFRACTION100
1.708-1.77640.31711400.2852657X-RAY DIFFRACTION100
1.7764-1.85720.31241400.24072673X-RAY DIFFRACTION100
1.8572-1.95510.26591410.21692669X-RAY DIFFRACTION100
1.9551-2.07760.24281400.19452668X-RAY DIFFRACTION100
2.0776-2.2380.22161430.16872707X-RAY DIFFRACTION100
2.238-2.46320.22391410.16372688X-RAY DIFFRACTION100
2.4632-2.81950.23641430.16962723X-RAY DIFFRACTION100
2.8195-3.55190.20171450.15042751X-RAY DIFFRACTION100
3.5519-38.06670.16041520.14592875X-RAY DIFFRACTION100

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