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- PDB-5u48: Wild-type Transthyretin in complex with 5-[(1E)-2-(4-Boronic acid... -

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Basic information

Entry
Database: PDB / ID: 5u48
TitleWild-type Transthyretin in complex with 5-[(1E)-2-(4-Boronic acid)ethenyl]-1,3-benzenediol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Boronic acids / Medicinal chemistry / stilbene / covalent ligand
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, 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-S4B / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3294
Polymers27,8172
Non-polymers5122
Water2,180121
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6588
Polymers55,6344
Non-polymers1,0244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.228, 84.947, 64.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-200-

S4B

21A-200-

S4B

31A-200-

S4B

41A-200-

S4B

51A-200-

S4B

61B-200-

S4B

71B-200-

S4B

81B-200-

S4B

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13908.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET32b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-S4B / {4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]phenyl}boronic acid


Mass: 256.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H13BO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.32 Å3/Da / Density % sol: 42.31 %
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-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→35.5 Å / Num. obs: 39026 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.16 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.5-1.537.30.68619040.8531100
1.53-1.557.30.6180.8841100
1.55-1.587.30.5130.921100
1.58-1.627.30.420.9351100
1.62-1.657.30.3870.9511100
1.65-1.697.30.3270.9611100
1.69-1.737.30.2820.9711100
1.73-1.787.30.2290.981100
1.78-1.837.30.1820.9861100
1.83-1.897.30.1420.9921100
1.89-1.967.30.1110.9941100
1.96-2.047.30.0950.9941100
2.04-2.137.40.0790.9971100
2.13-2.247.30.0730.9971100
2.24-2.387.30.0720.9961100
2.38-2.567.40.0580.9971100
2.56-2.827.30.0460.9981100
2.82-3.237.30.0360.9991100
3.23-4.077.20.0290.9991100
4.07-506.70.0290.999198.9

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Processing

Software
NameVersionClassification
HKL-20002.3.8data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXphenix.refine: 1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.5→35.5 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.78 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 3843 9.86 %Random 10%
Rwork0.1777 ---
obs0.1803 38984 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.22 Å2 / Biso mean: 23.9 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: final / Resolution: 1.5→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 38 121 1940
Biso mean--22.37 31.95 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071930
X-RAY DIFFRACTIONf_angle_d1.0462654
X-RAY DIFFRACTIONf_chiral_restr0.072297
X-RAY DIFFRACTIONf_plane_restr0.007345
X-RAY DIFFRACTIONf_dihedral_angle_d12.977688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4977-1.51670.26021410.23321238137997
1.5167-1.53660.27561440.234712861430100
1.5366-1.55770.2381340.214912841418100
1.5577-1.580.23451370.213812771414100
1.58-1.60350.22661500.203112771427100
1.6035-1.62860.24631470.199312601407100
1.6286-1.65530.20471300.198513231453100
1.6553-1.68380.25221400.19112731413100
1.6838-1.71450.2211610.184612601421100
1.7145-1.74740.23241460.187612921438100
1.7474-1.78310.22141360.188212951431100
1.7831-1.82190.19821390.185812781417100
1.8219-1.86420.2151400.186613161456100
1.8642-1.91090.20191300.175312941424100
1.9109-1.96250.20861370.176113111448100
1.9625-2.02030.22911360.174112991435100
2.0203-2.08550.22861440.186512871431100
2.0855-2.160.19621480.170213091457100
2.16-2.24650.2011380.17712921430100
2.2465-2.34870.19691560.170112891445100
2.3487-2.47250.21031500.178912901440100
2.4725-2.62730.22221330.186913361469100
2.6273-2.83010.21711520.183513131465100
2.8301-3.11480.24231320.184813481480100
3.1148-3.56510.16211450.163813321477100
3.5651-4.49030.16251470.147413501497100
4.4903-35.50070.20871500.1841432158299

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