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- PDB-4i89: Crystal structure of transthyretin in complex with diflunisal at ... -

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Basic information

Entry
Database: PDB / ID: 4i89
TitleCrystal structure of transthyretin in complex with diflunisal at acidic pH
ComponentsTransthyretin
Keywordstransport protein/inhibitor / amyloidosis / fibrillogenesis inhibitor / transthyretin stabilizers / T4 or T3 hormone / plasma / transport protein-inhibitor complex
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsZanotti, G. / Cendron, L. / Folli, C. / Florio, P. / Imbimbo, B.P. / Berni, R.
Citation
Journal: Febs Lett. / Year: 2013
Title: Structural evidence for native state stabilization of a conformationally labile amyloidogenic transthyretin variant by fibrillogenesis inhibitors.
Authors: Zanotti, G. / Cendron, L. / Folli, C. / Florio, P. / Imbimbo, B.P. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin.
Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.
Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / Berni, R.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Non-polymer description
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)28,0034
Polymers27,5032
Non-polymers5002
Water4,504250
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0068
Polymers55,0054
Non-polymers1,0014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8470 Å2
ΔGint-53 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 86.220, 64.320
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-201-

1FL

21A-201-

1FL

31A-201-

1FL

41B-367-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13751.280 Da / Num. of mol.: 2 / Fragment: Transthyretin (unp residues 21-147) / Mutation: I84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-1FL / 5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Diflunisal


Mass: 250.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8F2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 42.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 15% (w/v) PEG 2000 monomethylether, 0.1 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.69→32.93 Å / Num. all: 27383 / Num. obs: 27383 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3948 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I87

4i87


Resolution: 1.69→32.93 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1365 5.03 %random
Rwork0.1899 ---
obs0.1915 27111 99.04 %-
all-27383 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.731 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2799 Å2-0 Å20 Å2
2---0.9604 Å2-0 Å2
3---3.2404 Å2
Refinement stepCycle: LAST / Resolution: 1.69→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 36 250 2067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091882
X-RAY DIFFRACTIONf_angle_d1.2222573
X-RAY DIFFRACTIONf_dihedral_angle_d15.215650
X-RAY DIFFRACTIONf_chiral_restr0.091286
X-RAY DIFFRACTIONf_plane_restr0.008328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.75040.26551460.22932451X-RAY DIFFRACTION97
1.7504-1.82050.25381240.21212501X-RAY DIFFRACTION98
1.8205-1.90330.24911540.19572511X-RAY DIFFRACTION98
1.9033-2.00370.27881160.19152546X-RAY DIFFRACTION99
2.0037-2.12920.24151410.17842565X-RAY DIFFRACTION100
2.1292-2.29350.21151470.1852572X-RAY DIFFRACTION99
2.2935-2.52430.24151280.18852596X-RAY DIFFRACTION100
2.5243-2.88930.20941350.19712607X-RAY DIFFRACTION100
2.8893-3.63950.20911350.18082638X-RAY DIFFRACTION100
3.6395-32.93710.20251390.18912759X-RAY DIFFRACTION99

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