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- PDB-4l1t: Transthyretin in complex with (E)-3-(dimethylamino)-5-(4-hydroxy-... -

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Basic information

Entry
Database: PDB / ID: 4l1t
TitleTransthyretin in complex with (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzoic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Hormone transport protein / Thyroxine / Retinol
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) / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / 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 / 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-1WZ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: Biopolymers / Year: 2014
Title: Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging-what we know and what we need to learn.
Authors: Baranczak, A. / Connelly, S. / Liu, Y. / Choi, S. / Grimster, N.P. / Powers, E.T. / Wilson, I.A. / Kelly, J.W.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
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_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)28,1774
Polymers27,5552
Non-polymers6232
Water3,225179
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3558
Polymers55,1094
Non-polymers1,2464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6220 Å2
ΔGint-41 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.305, 85.551, 63.006
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-201-

1WZ

21A-201-

1WZ

31A-201-

1WZ

41B-201-

1WZ

51B-201-

1WZ

61B-201-

1WZ

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


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): Epicurian Gold / References: UniProt: P02766
#2: Chemical ChemComp-1WZ / 3-(dimethylamino)-5-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzoic acid / (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzoic acid


Mass: 311.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
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 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012
Details: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
RadiationMonochromator: ASYMMETRIC CUT 4.965 DEGS SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.16→37.92 Å / Num. obs: 78960 / % possible obs: 98.3 % / Redundancy: 6 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.034 / Net I/σ(I): 20.3
Reflection shellResolution: 1.16→1.22 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 10463 / Rsym value: 0.655 / % possible all: 90.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FBR

2fbr


Resolution: 1.16→37.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.12 / SU B: 1.038 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 3938 5 %RANDOM
Rwork0.1636 ---
obs0.1648 78787 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.28 Å2 / Biso mean: 18.4022 Å2 / Biso min: 4.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.16→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 46 179 2006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222055
X-RAY DIFFRACTIONr_bond_other_d0.0010.021360
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9712842
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0013360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50224.02387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19115335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5651510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_mcbond_it1.9481.51246
X-RAY DIFFRACTIONr_mcbond_other1.0261.5492
X-RAY DIFFRACTIONr_mcangle_it3.09122054
X-RAY DIFFRACTIONr_scbond_it3.633809
X-RAY DIFFRACTIONr_scangle_it5.4354.5763
X-RAY DIFFRACTIONr_rigid_bond_restr1.83333415
X-RAY DIFFRACTIONr_sphericity_free9.3133182
X-RAY DIFFRACTIONr_sphericity_bonded6.333338
LS refinement shellResolution: 1.158→1.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 211 -
Rwork0.307 4668 -
all-4879 -
obs--82.78 %

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