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- PDB-5u49: Wild-type Transthyretin in complex with 5-[(1E)-2-(2-Chloro-4-hyd... -

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Basic information

Entry
Database: PDB / ID: 5u49
TitleWild-type Transthyretin in complex with 5-[(1E)-2-(2-Chloro-4-hydroxyphenyl)ethenyl]-1,3-benzenediol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Boronic acids / Medicinal chemistry / stilbene / covalent ligand
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, 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
Similarity search - Domain/homology
Chem-S2L / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.22 Å
AuthorsWindsor, I.W. / Smith, T.P. / Raines, R.T. / Forest, K.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008349 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM044783 United States
National Science Foundation (NSF, United States)MCB 1518160 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Stilbene Boronic Acids Form a Covalent Bond with Human Transthyretin and Inhibit Its Aggregation.
Authors: Smith, T.P. / Windsor, I.W. / Forest, K.T. / Raines, R.T.
History
DepositionDec 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1712
Polymers13,9091
Non-polymers2631
Water19811
1
A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6858
Polymers55,6344
Non-polymers1,0514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Unit cell
Length a, b, c (Å)44.517, 65.895, 84.594
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-200-

S2L

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13908.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-S2L / 5-[(E)-2-(2-chloro-4-hydroxyphenyl)ethenyl]benzene-1,3-diol


Mass: 262.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11ClO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.3 M Sodium Citrate, 3.0% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.239801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.239801 Å / Relative weight: 1
ReflectionResolution: 2.22→33 Å / Num. obs: 5956 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.364 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.22-2.294.41.5373000.101198
2.29-2.334.72.7270.062199.3
2.33-2.385.52.8870.261199.7
2.38-2.426.15.9420.2121100
2.42-2.486.64.5590.32199.7
2.48-2.536.83.6430.3921100
2.53-2.672.5170.369199.7
2.6-2.676.81.5790.6241100
2.67-2.756.81.2320.262199.3
2.75-2.836.60.8770.756199.7
2.83-2.946.30.6550.7981100
2.94-3.055.80.5090.847199
3.05-3.195.60.3780.909185.5
3.19-3.366.50.270.96195.1
3.36-3.577.90.2610.973199.7
3.57-3.857.90.1990.9711100
3.85-4.237.80.1740.9811100
4.23-4.857.60.1460.9821100
4.85-6.17.60.140.985199.7
6.1-506.90.1070.978198.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementStarting model: pdbid 2QGB

2qgb


Resolution: 2.22→33 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.62
RfactorNum. reflection% reflectionSelection details
Rfree0.275 621 9.99 %Random 10%
Rwork0.202 ---
obs0.209 5919 96.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.56 Å2 / Biso mean: 41.2 Å2 / Biso min: 22.91 Å2
Refinement stepCycle: final / Resolution: 2.22→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 18 11 925
Biso mean--39.54 38.51 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008939
X-RAY DIFFRACTIONf_angle_d1.0441282
X-RAY DIFFRACTIONf_chiral_restr0.039143
X-RAY DIFFRACTIONf_plane_restr0.004163
X-RAY DIFFRACTIONf_dihedral_angle_d15.037325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2211-2.44460.31841460.24881311145793
2.4446-2.79820.31281560.23811406156299
2.7982-3.52480.27391500.20971368151895
3.5248-32.95110.25731690.181115131682100

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