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- PDB-4hjt: Kinetic stabilization of transthyretin through covalent modificat... -

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Basic information

Entry
Database: PDB / ID: 4hjt
TitleKinetic stabilization of transthyretin through covalent modification of K15 by (E)-N-(4-(4-hydroxy-3,5-dimethylstyryl)phenyl)propionamide
ComponentsTransthyretin
KeywordsHORMONE BINDING PROTEIN/INHIBITOR / HORMONE BINDING PROTEIN / Thyroxine / retinol binding protein / HORMONE BINDING PROTEIN-INHIBITOR complex
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-18A / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Stilbene vinyl sulfonamides as fluorogenic sensors of and traceless covalent kinetic stabilizers of transthyretin that prevent amyloidogenesis.
Authors: Suh, E.H. / Liu, Y. / Connelly, S. / Genereux, J.C. / Wilson, I.A. / Kelly, J.W.
History
DepositionOct 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Sep 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)28,1454
Polymers27,5552
Non-polymers5912
Water1,47782
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2918
Polymers55,1094
Non-polymers1,1824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6880 Å2
ΔGint-41 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.966, 85.157, 64.132
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-

18A

21A-201-

18A

31A-201-

18A

41A-201-

18A

51B-201-

18A

61B-201-

18A

71B-201-

18A

81B-201-

18A

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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: PALB, TTR / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-18A / N-{4-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]phenyl}propanamide / (E)-N-(4-(4-hydroxy-3,5-dimethylstyryl)phenyl)propionamide, bound form


Mass: 295.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 42.22 %
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 WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS ...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 WITH INHIBITORS 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: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2012 / Details: Rh coated flat mirror
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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→85.16 Å / Num. obs: 42818 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 55.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 4221 / Rsym value: 0.519 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FBR

2fbr


Resolution: 1.45→85.16 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1922 / WRfactor Rwork: 0.1698 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9088 / SU B: 1.802 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0772 / SU Rfree: 0.0634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2139 5.1 %RANDOM
Rwork0.1654 ---
obs0.1665 42350 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 156.33 Å2 / Biso mean: 23.2489 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å2-0 Å2
2---0.36 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.45→85.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 44 82 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222110
X-RAY DIFFRACTIONr_bond_other_d0.0010.021412
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.9792905
X-RAY DIFFRACTIONr_angle_other_deg0.95433482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1542490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59115332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3171510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212381
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02448
X-RAY DIFFRACTIONr_mcbond_it2.1981.51269
X-RAY DIFFRACTIONr_mcbond_other0.6191.5500
X-RAY DIFFRACTIONr_mcangle_it3.59622081
X-RAY DIFFRACTIONr_scbond_it4.6963841
X-RAY DIFFRACTIONr_scangle_it7.0764.5798
X-RAY DIFFRACTIONr_rigid_bond_restr1.90433522
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 164 -
Rwork0.269 2968 -
all-3132 -
obs--99.75 %

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