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- PDB-5u4b: Wild-type Transthyretin in complex with 3-[(1E)-2-(4-Hydroxypheny... -

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Basic information

Entry
Database: PDB / ID: 5u4b
TitleWild-type Transthyretin in complex with 3-[(1E)-2-(4-Hydroxyphenyl)ethenyl]benzoic Acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Boronic acid / Medicinal Chemistry / covalent inhibitor
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
3-[(E)-2-(4-hydroxyphenyl)ethenyl]benzoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.448 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)R01 GM044783 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008349 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)28,2984
Polymers27,8172
Non-polymers4812
Water2,828157
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5958
Polymers55,6344
Non-polymers9614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.052, 85.446, 64.107
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-200-

XOS

21A-200-

XOS

31A-200-

XOS

41A-200-

XOS

51A-200-

XOS

61A-200-

XOS

71B-200-

XOS

81B-200-

XOS

91B-200-

XOS

101B-200-

XOS

111B-200-

XOS

121B-200-

XOS

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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) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-XOS / 3-[(E)-2-(4-hydroxyphenyl)ethenyl]benzoic acid


Mass: 240.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.12 Å3/Da / Density % sol: 41.97 % / Mosaicity: 0.152 ° / Mosaicity esd: 0.002 °
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: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.448→38.5 Å / Num. obs: 42801 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.448-1.487.20.5410.8871100
1.48-1.57.30.4520.906199.1
1.5-1.537.20.3940.9331100
1.53-1.567.30.3380.95199.4
1.56-1.67.20.2850.965199.6
1.6-1.637.30.2550.9741100
1.63-1.677.30.2260.977199.8
1.67-1.727.30.2030.9791100
1.72-1.777.40.1720.984199.9
1.77-1.837.30.140.991199.9
1.83-1.897.30.1120.9931100
1.89-1.977.40.0960.9941100
1.97-2.067.40.0830.9951100
2.06-2.177.40.0720.9971100
2.17-2.37.40.0710.9961100
2.3-2.487.40.0670.9961100
2.48-2.737.30.0540.9981100
2.73-3.127.30.0430.9981100
3.12-3.947.20.0380.9991100
3.94-38.56.70.040.997199.7

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.448→38.447 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.82 / Stereochemistry target values: ML / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 4230 9.89 %Random 10%
Rwork0.1858 38522 --
obs0.1879 42752 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.38 Å2 / Biso mean: 19.4734 Å2 / Biso min: 8.91 Å2
Refinement stepCycle: final / Resolution: 1.448→38.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 36 157 1978
Biso mean--27.46 27.23 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071958
X-RAY DIFFRACTIONf_angle_d1.0342695
X-RAY DIFFRACTIONf_chiral_restr0.069302
X-RAY DIFFRACTIONf_plane_restr0.007351
X-RAY DIFFRACTIONf_dihedral_angle_d14.322707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4484-1.46490.29651250.25271215134097
1.4649-1.48210.26611540.24391277143199
1.4821-1.50020.24761260.2271254138099
1.5002-1.51920.25591220.223312981420100
1.5192-1.53920.26321440.22861260140499
1.5392-1.56030.27881460.231112341380100
1.5603-1.58250.24191510.208712681419100
1.5825-1.60620.25021420.20871251139399
1.6062-1.63130.24381510.20312491400100
1.6313-1.6580.25411300.21312951425100
1.658-1.68660.24421370.199512601397100
1.6866-1.71730.21461430.196313031446100
1.7173-1.75030.22421570.195712301387100
1.7503-1.7860.20911360.190312911427100
1.786-1.82490.22291320.193212641396100
1.8249-1.86730.21281340.195812821416100
1.8673-1.9140.17641470.18612881435100
1.914-1.96580.21991420.17812661408100
1.9658-2.02360.23321290.17913061435100
2.0236-2.08890.2051440.18712861430100
2.0889-2.16360.18341280.179712831411100
2.1636-2.25020.17721360.178612981434100
2.2502-2.35260.19411280.176513001428100
2.3526-2.47660.22241590.183512781437100
2.4766-2.63170.22211610.201612811442100
2.6317-2.83490.22461450.192313041449100
2.8349-3.120.23261430.197813141457100
3.12-3.57120.19291360.171413471483100
3.5712-4.49830.18281420.15313341476100
4.4983-38.4610.16221600.17941406156699

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