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- PDB-3fc8: Crystal structure of transthyretin in complex with iododiflunisal... -

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Basic information

Entry
Database: PDB / ID: 3fc8
TitleCrystal structure of transthyretin in complex with iododiflunisal-betaAlaOMe
Componentstransthyretin
KeywordsHORMONE BINDING PROTEIN / transthyretin / amyloid / inhibitors / iodine / Polymorphism / Polyneuropathy / Retinol-binding / Secreted
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
Chem-IFA / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGales, L. / Damas, A.M.
CitationJournal: Plos One / Year: 2009
Title: Iodine atoms: a new molecular feature for the design of potent transthyretin fibrillogenesis inhibitors.
Authors: Mairal, T. / Nieto, J. / Pinto, M. / Almeida, M.R. / Gales, L. / Ballesteros, A. / Barluenga, J. / Perez, J.J. / Vazquez, J.T. / Centeno, N.B. / Saraiva, M.J. / Damas, A.M. / Planas, A. / ...Authors: Mairal, T. / Nieto, J. / Pinto, M. / Almeida, M.R. / Gales, L. / Ballesteros, A. / Barluenga, J. / Perez, J.J. / Vazquez, J.T. / Centeno, N.B. / Saraiva, M.J. / Damas, A.M. / Planas, A. / Arsequell, G. / Valencia, G.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
A: transthyretin
B: transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7664
Polymers26,8442
Non-polymers9222
Water1,74797
1
A: transthyretin
B: transthyretin
hetero molecules

A: transthyretin
B: transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5338
Polymers53,6884
Non-polymers1,8454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9500 Å2
ΔGint-60 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.238, 85.102, 63.064
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-3000-

IFA

21A-3000-

IFA

31A-3000-

IFA

41A-3000-

IFA

51A-3000-

IFA

61A-3000-

IFA

71B-2000-

IFA

81B-2000-

IFA

91B-2000-

IFA

101B-2000-

IFA

111B-2000-

IFA

121B-2000-

IFA

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Components

#1: Protein transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13421.952 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Iododiflunisal-betaAlaOMe binds in the hormone binding channel
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-IFA / METHYL N-[(2',4'-DIFLUORO-4-HYDROXY-5-IODOBIPHENYL-3-YL)CARBONYL]-BETA-ALANINATE


Mass: 461.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14F2INO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2.0 M ammonium sulfate, 7% glycerol and 0.2 M sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.85→563.12 Å / Num. all: 18982 / Num. obs: 18945 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 32.4
Reflection shellResolution: 1.85→1.898 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F86

1f86


Resolution: 1.85→63.12 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.511 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21019 1025 5.1 %RANDOM
Rwork0.19553 ---
all0.19945 18982 --
obs0.19628 18982 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 50 97 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9692472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.49423.2259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.462154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2719
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21220
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1271.51148
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07121847
X-RAY DIFFRACTIONr_scbond_it2.8873814
X-RAY DIFFRACTIONr_scangle_it4.5324.5625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 72 -
Rwork0.217 1365 -
obs--100 %

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