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- PDB-4fi6: Kinetic Stabilization of transthyretin through covalent modificat... -

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Basic information

Entry
Database: PDB / ID: 4fi6
TitleKinetic Stabilization of transthyretin through covalent modification of K15 by 3-(5-(3,5-dichlorophenyl)-1,3,4-oxadiazol-2-yl)-benzenesulfonamide
ComponentsTransthyretin
KeywordsHORMONE/HORMONE INHIBITOR / hormone / binding protein / Kinetic stabilizer complex / HORMONE-HORMONE INHIBITOR complex
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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-0U7 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsConnelly, S. / Grimster, N. / Wilson, I.A. / Kelly, J.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Aromatic Sulfonyl Fluorides Covalently Kinetically Stabilize Transthyretin to Prevent Amyloidogenesis while Affording a Fluorescent Conjugate.
Authors: Grimster, N.P. / Connelly, S. / Baranczak, A. / Dong, J. / Krasnova, L.B. / Sharpless, K.B. / Powers, E.T. / Wilson, I.A. / Kelly, J.W.
History
DepositionJun 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3Jan 29, 2014Group: Other
Revision 1.4Sep 13, 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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,3014
Polymers27,5552
Non-polymers7462
Water2,990166
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6028
Polymers55,1094
Non-polymers1,4934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6250 Å2
ΔGint-41 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.903, 85.294, 63.758
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-301-

0U7

21A-301-

0U7

31A-301-

0U7

41A-301-

0U7

51B-301-

0U7

61B-301-

0U7

71B-301-

0U7

81A-417-

HOH

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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): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-0U7 / 3-[5-(3,5-dichlorophenyl)-1,3,4-oxadiazol-2-yl]benzenesulfonyl fluoride


Mass: 373.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7Cl2FN2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details0U7 UNDERGOES NUCLEOPHILIC ATTACK BY LYS 15 RESULTING IN A COVALENT ATTACHMENT AND F REMOVED

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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: 2.12 Å3/Da / Density % sol: 41.89 %
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 298.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 24, 2011
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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→85.294 Å / Num. obs: 41391 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 40.5
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 4083 / Rsym value: 0.478 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FBR

2fbr


Resolution: 1.46→85.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1952 / WRfactor Rwork: 0.1664 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.9005 / SU B: 2.041 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0786 / SU Rfree: 0.0635 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 2078 5 %RANDOM
Rwork0.1602 ---
obs0.1614 41245 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 113.22 Å2 / Biso mean: 24.2622 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å20 Å2
2---0.9 Å2-0 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.46→85.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 44 166 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222070
X-RAY DIFFRACTIONr_bond_other_d0.0010.021385
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9822871
X-RAY DIFFRACTIONr_angle_other_deg0.91433414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.10524.06691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7191511
X-RAY DIFFRACTIONr_chiral_restr0.110.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02435
X-RAY DIFFRACTIONr_mcbond_it1.9741.51242
X-RAY DIFFRACTIONr_mcbond_other0.5641.5496
X-RAY DIFFRACTIONr_mcangle_it3.20122052
X-RAY DIFFRACTIONr_scbond_it4.4593828
X-RAY DIFFRACTIONr_scangle_it6.7134.5790
X-RAY DIFFRACTIONr_rigid_bond_restr1.79533455
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 143 -
Rwork0.229 2863 -
all-3006 -
obs--98.98 %

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