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- PDB-5u4g: Wild-type Transthyretin in complex with 2-Boronic Acid-1-[(1E)-2-... -

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Basic information

Entry
Database: PDB / ID: 5u4g
TitleWild-type Transthyretin in complex with 2-Boronic Acid-1-[(1E)-2-(3-boronic acid)ethenyl]-4-chlorobenzene
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) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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-7UV / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,3904
Polymers27,8172
Non-polymers5732
Water1,946108
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7808
Polymers55,6344
Non-polymers1,1454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.019, 85.118, 64.023
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-

7UV

21A-200-

7UV

31B-200-

7UV

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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-7UV / (3-{(E)-2-[2-chloro-4-(hydroxyboranyl)phenyl]ethenyl}phenyl)boronic acid


Mass: 286.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13B2ClO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.62 % / Mosaicity: 0.481 ° / Mosaicity esd: 0.005 °
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: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22450 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
1.8-1.837.30.47710870.917199.4
1.83-1.867.40.4060.935199.3
1.86-1.97.30.3010.962199.5
1.9-1.947.30.2670.967199.6
1.94-1.987.40.2130.981199.5
1.98-2.037.40.1880.984199.7
2.03-2.087.40.1620.99199.7
2.08-2.137.40.1350.992199.8
2.13-2.27.30.1130.994199.8
2.2-2.277.30.10.995199.8
2.27-2.357.40.0950.995199.9
2.35-2.447.30.0860.997199.9
2.44-2.557.30.0810.9961100
2.55-2.697.30.0760.9971100
2.69-2.867.30.0740.9951100
2.86-3.087.30.0680.9971100
3.08-3.397.30.0570.9981100
3.39-3.887.20.0370.9991100
3.88-4.887.10.02311100
4.88-506.60.0211198.2

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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: 1.8→38.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.97
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2189 9.76 %Random 10%
Rwork0.188 ---
obs0.191 22421 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.45 Å2 / Biso mean: 27.6 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 1.8→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 40 108 1933
Biso mean--30.47 32.61 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091896
X-RAY DIFFRACTIONf_angle_d1.2072591
X-RAY DIFFRACTIONf_chiral_restr0.054289
X-RAY DIFFRACTIONf_plane_restr0.007333
X-RAY DIFFRACTIONf_dihedral_angle_d16.491661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7971-1.83620.28131300.24561157128794
1.8362-1.87890.2921300.22311256138699
1.8789-1.92590.2551420.210812241366100
1.9259-1.9780.25871360.20231246138299
1.978-2.03620.24471240.203312481372100
2.0362-2.10190.2261480.191812341382100
2.1019-2.1770.22391420.188512611403100
2.177-2.26420.2311440.184612571401100
2.2642-2.36720.25381410.186412591400100
2.3672-2.4920.22721330.195212631396100
2.492-2.64810.24011100.198912881398100
2.6481-2.85250.21881360.198212841420100
2.8525-3.13940.23431390.203312771416100
3.1394-3.59340.21471450.173912951440100
3.5934-4.52620.20081420.150213081450100
4.5262-38.40280.19631470.19581375152299

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