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- PDB-7acu: Crystal structure of human transthyretin in complex with Benzbromarone -

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Basic information

Entry
Database: PDB / ID: 7acu
TitleCrystal structure of human transthyretin in complex with Benzbromarone
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / TTR / benzbromarone / complex
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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-R75 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.541 Å
AuthorsLeite, J.P. / Gales, L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)SFRH/BD/129921/2017 Portugal
CitationJournal: Int J Mol Sci / Year: 2020
Title: Repurposing Benzbromarone for Familial Amyloid Polyneuropathy: A New Transthyretin Tetramer Stabilizer.
Authors: Cotrina, E.Y. / Oliveira, A. / Leite, J.P. / Llop, J. / Gales, L. / Quintana, J. / Cardoso, I. / Arsequell, G.
History
DepositionSep 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)26,0604
Polymers25,2122
Non-polymers8482
Water2,000111
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1218
Polymers50,4244
Non-polymers1,6964
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Unit cell
Length a, b, c (Å)42.500, 85.190, 64.080
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSGLUGLU(chain 'A' and (resid 10 through 73 or resid 75 through 124))AA10 - 721 - 63
12THRTHRTHRTHR(chain 'A' and (resid 10 through 73 or resid 75 through 124))AA75 - 12366 - 114
23CYSCYSGLUGLU(chain 'B' and (resid 10 through 73 or resid 75 through 124))BB10 - 721 - 63
24THRTHRTHRTHR(chain 'B' and (resid 10 through 73 or resid 75 through 124))BB75 - 12366 - 114

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 12606.103 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 (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-R75 / [3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-1-benzofuran-3-yl)methanone / Benzbromarone / Benzbromarone


Mass: 424.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12Br2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiarrhythmic, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2 M acetate buffer pH 4.8, 2.2 M ammonium sulfate, 7% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.35→64.39 Å / Num. obs: 52367 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.13 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.1
Reflection shellResolution: 1.35→64.39 Å / Rmerge(I) obs: 0.071 / Num. unique obs: 321843

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y1D

1y1d


Resolution: 1.541→35.47 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 2.2 / Phase error: 19.3296
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1738 4.95 %
Rwork0.1824 33375 -
obs0.1839 35120 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.43 Å2
Refinement stepCycle: LAST / Resolution: 1.541→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 44 111 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621876
X-RAY DIFFRACTIONf_angle_d1.25712566
X-RAY DIFFRACTIONf_chiral_restr0.0667285
X-RAY DIFFRACTIONf_plane_restr0.0072322
X-RAY DIFFRACTIONf_dihedral_angle_d15.3324268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.28111490.2492749X-RAY DIFFRACTION99.93
1.59-1.640.2491630.22262734X-RAY DIFFRACTION100
1.64-1.70.261420.21512716X-RAY DIFFRACTION99.97
1.7-1.760.25531240.21412757X-RAY DIFFRACTION99.97
1.76-1.840.25131500.19842741X-RAY DIFFRACTION99.86
1.84-1.940.20611430.17262763X-RAY DIFFRACTION99.97
1.94-2.060.19311480.17322738X-RAY DIFFRACTION99.97
2.06-2.220.18141430.17062796X-RAY DIFFRACTION99.93
2.22-2.450.19361410.18022776X-RAY DIFFRACTION99.97
2.45-2.80.21871550.18052803X-RAY DIFFRACTION99.86
2.8-3.530.20981320.17042832X-RAY DIFFRACTION99.93
3.53-38.030.21311480.18092970X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: -22.1749506108 Å / Origin y: 55.2034672258 Å / Origin z: 48.1791623173 Å
111213212223313233
T0.108018715307 Å20.00684357310974 Å20.0188439021915 Å2-0.0998381693594 Å20.00814528660568 Å2--0.141293845317 Å2
L1.00427285295 °20.0102490114067 °20.663866193343 °2-1.41180451727 °20.0665507026123 °2--1.42583699893 °2
S-0.0412113006714 Å °0.0515425351413 Å °0.176969276633 Å °-0.0381398273299 Å °-0.0488985238332 Å °0.0164418231937 Å °-0.0921188649133 Å °0.0349691911091 Å °0.0563064684024 Å °
Refinement TLS groupSelection details: all

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