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- PDB-5u4d: Wild-type Transthyretin in complex with 3-[(1E)-2-(2-Chloro-4-hyd... -

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Basic information

Entry
Database: PDB / ID: 5u4d
TitleWild-type Transthyretin in complex with 3-[(1E)-2-(2-Chloro-4-hydroxyphenyl)ethenyl]benzoic Acid
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-XLO / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)28,3674
Polymers27,8172
Non-polymers5492
Water2,342130
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7338
Polymers55,6344
Non-polymers1,0994
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.207, 84.814, 64.618
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-

XLO

21B-200-

XLO

31B-200-

XLO

41B-200-

XLO

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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-XLO / 3-[(E)-2-(2-chloro-4-hydroxyphenyl)ethenyl]benzoic acid


Mass: 274.699 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11ClO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 42.2 % / Mosaicity: 0.188 ° / Mosaicity esd: 0.003 °
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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→38.5 Å / Num. obs: 35258 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 19.21 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.55-1.585.20.60717350.73199.5
1.58-1.615.90.5250.838199.9
1.61-1.646.20.4740.8821100
1.64-1.676.20.4350.8831100
1.67-1.716.20.3710.9231100
1.71-1.756.20.3030.941100
1.75-1.796.20.2520.9511100
1.79-1.846.20.2010.9731100
1.84-1.896.20.1570.9821100
1.89-1.956.30.1290.9861100
1.95-2.026.20.1190.9851100
2.02-2.16.20.1080.9911100
2.1-2.26.30.0910.9931100
2.2-2.326.30.080.9931100
2.32-2.466.30.0760.9951100
2.46-2.656.20.0750.994199.9
2.65-2.926.20.0720.9961100
2.92-3.346.20.0580.9961100
3.34-4.216.10.0450.998199.8
4.21-505.80.0380.998197.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXphenix.refine: 1.9_1692refinement
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.55→38.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.03 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3474 9.87 %Random 10%
Rwork0.206 ---
obs0.21 35214 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91 Å2 / Biso mean: 26.4 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.55→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 38 130 1953
Biso mean--26.63 34.14 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071916
X-RAY DIFFRACTIONf_angle_d1.0382627
X-RAY DIFFRACTIONf_chiral_restr0.041293
X-RAY DIFFRACTIONf_plane_restr0.006339
X-RAY DIFFRACTIONf_dihedral_angle_d15.392679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5489-1.57020.35581280.30331220134897
1.5702-1.59260.30411560.283512421398100
1.5926-1.61640.3071550.258912301385100
1.6164-1.64160.3231420.273612451387100
1.6416-1.66850.291320.273212761408100
1.6685-1.69730.32541350.253412441379100
1.6973-1.72820.28681470.250412561403100
1.7282-1.76140.31711320.24812441376100
1.7614-1.79740.27021510.243312661417100
1.7974-1.83640.25121240.235212351359100
1.8364-1.87920.27291420.237812721414100
1.8792-1.92620.23041070.228812811388100
1.9262-1.97820.27161520.220212581410100
1.9782-2.03640.27441340.225812711405100
2.0364-2.10220.23111400.218312421382100
2.1022-2.17730.22611270.200213011428100
2.1773-2.26450.22231340.204812651399100
2.2645-2.36750.22061460.203712721418100
2.3675-2.49230.27441450.207212691414100
2.4923-2.64840.25571480.214812631411100
2.6484-2.85280.27371210.214513091430100
2.8528-3.13980.24841490.203812901439100
3.1398-3.59390.21231470.178613051452100
3.5939-4.52680.22241340.158613191453100
4.5268-38.5110.20041460.19571365151197

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