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- PDB-8ii4: Crystal structure of V30M-TTR in complex with 6-hydroxy BBM -

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Basic information

Entry
Database: PDB / ID: 8ii4
TitleCrystal structure of V30M-TTR in complex with 6-hydroxy BBM
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine / amyloidosis / inhibitor
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-PKQ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsYokoyama, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem. / Year: 2023
Title: Benziodarone and 6-hydroxybenziodarone are potent and selective inhibitors of transthyretin amyloidogenesis.
Authors: Mizuguchi, M. / Yokoyama, T. / Okada, T. / Nakagawa, Y. / Fujii, K. / Nabeshima, Y. / Toyooka, N.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)35,5654
Polymers34,6852
Non-polymers8802
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.264, 85.656, 63.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

PKQ

21A-201-

PKQ

31B-201-

PKQ

41B-201-

PKQ

51B-201-

PKQ

61B-201-

PKQ

71B-201-

PKQ

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-PKQ / [3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-6-oxidanyl-1-benzofuran-3-yl)methanone


Mass: 440.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12Br2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.71 Å3/Da / Density % sol: 27.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, CaCl2, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.499→38.62 Å / Num. obs: 38780 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rrim(I) all: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 1.499→1.55 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3764 / CC1/2: 0.856 / Rrim(I) all: 0.733

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→30.437 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 1937 5 %
Rwork0.1827 --
obs0.1835 38738 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→30.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 46 167 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071921
X-RAY DIFFRACTIONf_angle_d1.0582630
X-RAY DIFFRACTIONf_dihedral_angle_d23.015678
X-RAY DIFFRACTIONf_chiral_restr0.083282
X-RAY DIFFRACTIONf_plane_restr0.007327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4991-1.53660.25461330.24122540X-RAY DIFFRACTION98
1.5366-1.57810.30041370.23442595X-RAY DIFFRACTION100
1.5781-1.62460.24771360.21472578X-RAY DIFFRACTION100
1.6246-1.6770.23351380.20752625X-RAY DIFFRACTION100
1.677-1.73690.22691360.19472589X-RAY DIFFRACTION100
1.7369-1.80650.22431380.18952607X-RAY DIFFRACTION100
1.8065-1.88870.21191370.18052610X-RAY DIFFRACTION100
1.8887-1.98820.19321380.17222617X-RAY DIFFRACTION100
1.9882-2.11280.22841360.1772596X-RAY DIFFRACTION100
2.1128-2.27590.19071390.17182652X-RAY DIFFRACTION100
2.2759-2.50480.24371390.1812636X-RAY DIFFRACTION100
2.5048-2.8670.20691400.192653X-RAY DIFFRACTION100
2.867-3.61120.17161420.18032701X-RAY DIFFRACTION100
3.6112-30.4370.18021480.17642802X-RAY DIFFRACTION99

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