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- PDB-6u0q: Transthyretin in complex with (E)-5,5'-(ethene-1,2-diyl)bis(1,1-d... -

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Basic information

Entry
Database: PDB / ID: 6u0q
TitleTransthyretin in complex with (E)-5,5'-(ethene-1,2-diyl)bis(1,1-dihydroxy-3-oxo-1,3-dihydrobenzo[c][1,2]oxaborol-1-uide)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / boronic acid / covalent inhibitor
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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-S2B / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWindsor, I.W. / Graham, B.J. / Raines, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM044783 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Boronic acid with high oxidative stability and utility in biological contexts.
Authors: Graham, B.J. / Windsor, I.W. / Gold, B. / Raines, R.T.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 18, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5254
Polymers27,8172
Non-polymers7082
Water3,207178
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0508
Polymers55,6344
Non-polymers1,4164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.090, 85.840, 64.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
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-201-

S2B

21A-201-

S2B

31A-201-

S2B

41B-201-

S2B

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-S2B / 3-[(~{E})-2-[7,7-bis(oxidanyl)-9-oxidanylidene-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-3-yl]ethenyl]-7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-9-one


Mass: 353.884 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12B2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.3 M sodium citrate, 2% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→30.41 Å / Num. obs: 24767 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Net I/σ(I): 17.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2431 / CC1/2: 0.794 / R split: 0.278 / Rpim(I) all: 0.278 / Rrim(I) all: 0.481 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5u4f

5u4f


Resolution: 1.75→30.41 Å / SU ML: 0.2035 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8174
RfactorNum. reflection% reflection
Rfree0.2224 1555 6.29 %
Rwork0.178 --
obs0.1807 24740 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.37 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 48 178 2011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.28881410.24792091X-RAY DIFFRACTION99.96
1.81-1.870.29941380.2372046X-RAY DIFFRACTION100
1.87-1.950.25791380.19082068X-RAY DIFFRACTION99.95
1.95-2.030.2421400.18732090X-RAY DIFFRACTION100
2.03-2.140.21091400.18882085X-RAY DIFFRACTION100
2.14-2.280.21471390.18142083X-RAY DIFFRACTION99.96
2.28-2.450.2531410.18132090X-RAY DIFFRACTION100
2.45-2.70.24631410.19152109X-RAY DIFFRACTION100
2.7-3.090.21171420.18342125X-RAY DIFFRACTION100
3.09-3.890.18691430.15442138X-RAY DIFFRACTION100
3.89-30.410.20461520.15692260X-RAY DIFFRACTION99.92

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