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- PDB-3imt: Transthyretin in complex with (E)-4-(4-aminostyryl)-2,6-dibromophenol -

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Basic information

Entry
Database: PDB / ID: 3imt
TitleTransthyretin in complex with (E)-4-(4-aminostyryl)-2,6-dibromophenol
ComponentsTransthyretin
KeywordsHORMONE / Growth Factor / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
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
Chem-IW3 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsConnelly, S. / Wilson, I.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: A substructure combination strategy to create potent and selective transthyretin kinetic stabilizers that prevent amyloidogenesis and cytotoxicity.
Authors: Choi, S. / Reixach, N. / Connelly, S. / Johnson, S.M. / Wilson, I.A. / Kelly, J.W.
History
DepositionAug 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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)28,2934
Polymers27,5552
Non-polymers7382
Water2,378132
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5868
Polymers55,1094
Non-polymers1,4764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.260, 84.785, 63.238
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-128-

IW3

21A-128-

IW3

31A-128-

IW3

41B-128-

IW3

51B-128-

IW3

61B-128-

IW3

71B-128-

IW3

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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) / Gene: TTR, PALB / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicuran gold / References: UniProt: P02766
#2: Chemical ChemComp-IW3 / 4-[(E)-2-(4-aminophenyl)ethenyl]-2,6-dibromophenol


Mass: 369.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11Br2NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1. ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.4→84.82 Å / Num. obs: 44988 / % possible obs: 98.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.05 / Net I/σ(I): 28.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4391 / Rsym value: 0.574 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QGB

2qgb


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.897 / SU R Cruickshank DPI: 0.07 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2257 5 %RANDOM
Rwork0.164 ---
obs0.165 44959 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.27 Å2 / Biso mean: 21.608 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.7 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 72 132 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222060
X-RAY DIFFRACTIONr_bond_other_d00.021363
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9842841
X-RAY DIFFRACTIONr_angle_other_deg4.3163.0033316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41624.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3415329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0651510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212357
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02409
X-RAY DIFFRACTIONr_mcbond_it1.8741.51223
X-RAY DIFFRACTIONr_mcbond_other2.9841.5490
X-RAY DIFFRACTIONr_mcangle_it2.89322012
X-RAY DIFFRACTIONr_scbond_it3.7963837
X-RAY DIFFRACTIONr_scangle_it5.6014.5806
X-RAY DIFFRACTIONr_rigid_bond_restr2.45933423
X-RAY DIFFRACTIONr_sphericity_free9.7813134
X-RAY DIFFRACTIONr_sphericity_bonded4.30633346
LS refinement shellResolution: 1.4→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 154 -
Rwork0.214 2843 -
all-2997 -
obs--89.6 %

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