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- PDB-3b56: Crystal structure of transthyretin in complex with 3,5-diiodosali... -

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Basic information

Entry
Database: PDB / ID: 3b56
TitleCrystal structure of transthyretin in complex with 3,5-diiodosalicylic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TRANSTHYRETIN / AMYLOID INHIBITORS / IODINE / Disease mutation / Glycoprotein / Hormone / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase 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/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
2-HYDROXY-3,5-DIIODO-BENZOIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGales, L. / Damas, A.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Iodination of salicylic acid improves its binding to transthyretin
Authors: Gales, L. / Almeida, M.R. / Arsequell, G. / Valencia, G. / Saraiva, M.J. / Damas, A.M.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3354
Polymers27,5552
Non-polymers7802
Water3,405189
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6698
Polymers55,1094
Non-polymers1,5604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area8220 Å2
ΔGint-29 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.539, 85.757, 64.346
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-2000-

DIU

21B-3000-

DIU

31B-3000-

DIU

41B-3000-

DIU

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Components

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


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pINTR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02766
#2: Chemical ChemComp-DIU / 2-HYDROXY-3,5-DIIODO-BENZOIC ACID / 2-HYDROXY-3,5-DIIODOBENZOIC ACID


Mass: 389.914 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4I2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 200mM acetate buffer, 2.2M ammonium sulfate, 7% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.55→28.58 Å / Num. all: 34993 / Num. obs: 34958 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F86

1f86


Resolution: 1.55→27.34 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.283 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21368 1756 5 %RANDOM
Rwork0.18917 ---
obs0.19043 33166 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 24 189 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221779
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9542434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56723.55959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.553154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021340
X-RAY DIFFRACTIONr_nbd_refined0.2020.2702
X-RAY DIFFRACTIONr_nbtor_refined0.310.21204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.224
X-RAY DIFFRACTIONr_mcbond_it0.7891.51143
X-RAY DIFFRACTIONr_mcangle_it1.4921847
X-RAY DIFFRACTIONr_scbond_it2.1053725
X-RAY DIFFRACTIONr_scangle_it3.2814.5587
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 95 -
Rwork0.227 2458 -
obs--99.92 %

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