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- PDB-3ims: Transthyretin in complex with 2,6-dibromo-4-(2,6-dichlorophenethy... -

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Basic information

Entry
Database: PDB / ID: 3ims
TitleTransthyretin in complex with 2,6-dibromo-4-(2,6-dichlorophenethyl)phenol
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
2,6-dibromo-4-[2-(2,6-dichlorophenyl)ethyl]phenol / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsConnelly, S. / Wilson, I.A.
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)28,4054
Polymers27,5552
Non-polymers8502
Water2,666148
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8098
Polymers55,1094
Non-polymers1,7004
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.500, 85.110, 63.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-128-

IW2

21A-128-

IW2

31B-128-

IW2

41B-128-

IW2

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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): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-IW2 / 2,6-dibromo-4-[2-(2,6-dichlorophenyl)ethyl]phenol


Mass: 424.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10Br2Cl2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.4→63.37 Å / Num. obs: 45887 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.04 / Net I/σ(I): 26.1

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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: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.888 / SU B: 1.857 / SU ML: 0.034 / SU R Cruickshank DPI: 0.068 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2332 5.1 %RANDOM
Rwork0.165 ---
obs0.167 43555 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.58 Å2 / Biso mean: 18.912 Å2 / Biso min: 7.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 38 148 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221976
X-RAY DIFFRACTIONr_bond_other_d0.0010.021304
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9652719
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0023183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89924.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61915312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.442159
X-RAY DIFFRACTIONr_chiral_restr0.1110.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022241
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02398
X-RAY DIFFRACTIONr_nbd_refined0.2240.2313
X-RAY DIFFRACTIONr_nbd_other0.20.21274
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2949
X-RAY DIFFRACTIONr_nbtor_other0.0890.21071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.221
X-RAY DIFFRACTIONr_mcbond_it2.4541.51547
X-RAY DIFFRACTIONr_mcbond_other0.871.5483
X-RAY DIFFRACTIONr_mcangle_it2.86121969
X-RAY DIFFRACTIONr_scbond_it4.3413953
X-RAY DIFFRACTIONr_scangle_it5.3644.5734
X-RAY DIFFRACTIONr_rigid_bond_restr2.56234118
X-RAY DIFFRACTIONr_sphericity_free9.8723150
X-RAY DIFFRACTIONr_sphericity_bonded4.55933212
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 177 -
Rwork0.198 3170 -
all-3347 -
obs--99.64 %

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