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- PDB-5u4e: Wild-type Transthyretin in complex with 3-[(1E)-2-(2-Chloro-4-bor... -

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Basic information

Entry
Database: PDB / ID: 5u4e
TitleWild-type Transthyretin in complex with 3-[(1E)-2-(2-Chloro-4-boronic acid)ethenyl]benzoic Acid
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-XLB / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)28,4224
Polymers27,8172
Non-polymers6052
Water3,045169
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8448
Polymers55,6344
Non-polymers1,2104
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area6910 Å2
ΔGint-40 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.029, 85.861, 63.831
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-

XLB

21A-200-

XLB

31A-200-

XLB

41B-200-

XLB

51B-200-

XLB

61B-200-

XLB

71B-200-

XLB

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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-XLB / 3-[(E)-2-(4-borono-2-chlorophenyl)ethenyl]benzoic acid


Mass: 302.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12BClO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 0.449 ° / Mosaicity esd: 0.004 °
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 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→26 Å / Num. obs: 42788 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.45-1.487.10.61220940.859199.9
1.48-1.57.10.5140.8821100
1.5-1.537.20.4440.9221100
1.53-1.567.20.3770.941100
1.56-1.67.20.310.9591100
1.6-1.637.30.2750.9711100
1.63-1.677.30.2450.9721100
1.67-1.727.30.2150.9791100
1.72-1.777.30.1730.9851100
1.77-1.837.30.1440.9891100
1.83-1.897.30.1130.9931100
1.89-1.977.30.0960.9951100
1.97-2.067.30.080.9951100
2.06-2.177.30.0670.9971100
2.17-2.37.30.0640.9961100
2.3-2.487.30.0550.9981100
2.48-2.737.30.0430.9991100
2.73-3.127.30.0320.9991100
3.12-3.947.20.0260.999199.9
3.94-506.70.0270.999199.5

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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: 1.45→26 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.84
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4229 9.9 %Random 10%
Rwork0.18 ---
obs0.182 42733 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.35 Å2 / Biso mean: 19.8 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 1.45→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 84 169 2038
Biso mean--20.08 28.61 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072052
X-RAY DIFFRACTIONf_angle_d1.1632823
X-RAY DIFFRACTIONf_chiral_restr0.076307
X-RAY DIFFRACTIONf_plane_restr0.007371
X-RAY DIFFRACTIONf_dihedral_angle_d15.93730
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 (%)
1.4491-1.46550.29041280.25911234136297
1.4655-1.48280.28291520.24512791431100
1.4828-1.50080.25171250.226712341359100
1.5008-1.51980.23951270.221512901417100
1.5198-1.53980.26111410.2212801421100
1.5398-1.56090.28311510.212212341385100
1.5609-1.58320.23631450.203312551400100
1.5832-1.60680.21971410.192412761417100
1.6068-1.6320.22171520.18812591411100
1.632-1.65870.23451280.198212801408100
1.6587-1.68730.24611390.186712711410100
1.6873-1.7180.24281500.192912761426100
1.718-1.7510.22371480.185512451393100
1.751-1.78670.2231360.182612981434100
1.7867-1.82560.20711320.185712631395100
1.8256-1.8680.17821400.185712821422100
1.868-1.91470.17711340.180912691403100
1.9147-1.96650.22321550.179412731428100
1.9665-2.02430.2421270.172613031430100
2.0243-2.08960.17561410.174612721413100
2.0896-2.16430.18021270.165812901417100
2.1643-2.25090.17741390.175513001439100
2.2509-2.35330.181270.164312951422100
2.3533-2.47730.22591580.175512731431100
2.4773-2.63230.21211590.194912771436100
2.6323-2.83530.21091470.196213061453100
2.8353-3.12020.20691410.192113121453100
3.1202-3.57070.18151370.157313411478100
3.5707-4.49470.17821420.147513331475100
4.4947-25.63790.14871600.18341404156499

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