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- PDB-8w46: X-ray crystal structure of V30M-TTR in complex with pterostilbene -

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Basic information

Entry
Database: PDB / ID: 8w46
TitleX-ray crystal structure of V30M-TTR in complex with pterostilbene
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidogenesis / thyroid hormone 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
Pterostilbene / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsYokoyama, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin.
Authors: Yokoyama, T. / Kusaka, K. / Mizuguchi, M. / Nabeshima, Y. / Fujiwara, S.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)35,4776
Polymers34,6852
Non-polymers7924
Water3,279182
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,95412
Polymers69,3704
Non-polymers1,5848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.055, 84.753, 63.534
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-

3RL

21A-201-

3RL

31B-200-

3RL

41B-200-

3RL

51B-200-

3RL

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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-3RL / Pterostilbene


Mass: 256.296 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H16O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.67 Å3/Da / Density % sol: 26.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Disodium malonate, 0.1M NaOAc pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→35.25 Å / Num. obs: 51890 / % possible obs: 99.74 % / Redundancy: 7.09 % / CC1/2: 1 / Rpim(I) all: 0.012 / Rrim(I) all: 0.031 / Net I/σ(I): 28.7
Reflection shellResolution: 1.35→1.4 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 4993 / CC1/2: 0.884 / Rpim(I) all: 0.24 / Rrim(I) all: 0.649

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→32.855 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1878 2595 5 %
Rwork0.1637 --
obs0.1648 51883 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→32.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 58 182 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051878
X-RAY DIFFRACTIONf_angle_d0.7762556
X-RAY DIFFRACTIONf_dihedral_angle_d18.655663
X-RAY DIFFRACTIONf_chiral_restr0.088282
X-RAY DIFFRACTIONf_plane_restr0.006323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3730.25051280.20672440X-RAY DIFFRACTION96
1.373-1.39940.20821350.17862546X-RAY DIFFRACTION100
1.3994-1.42790.23051360.1812592X-RAY DIFFRACTION100
1.4279-1.4590.19741340.16112540X-RAY DIFFRACTION100
1.459-1.49290.21761350.15972572X-RAY DIFFRACTION100
1.4929-1.53020.18131360.14822577X-RAY DIFFRACTION100
1.5302-1.57160.1831350.14182566X-RAY DIFFRACTION100
1.5716-1.61790.18461350.13752564X-RAY DIFFRACTION100
1.6179-1.67010.20921370.1382611X-RAY DIFFRACTION100
1.6701-1.72980.18641360.1522576X-RAY DIFFRACTION100
1.7298-1.7990.21581350.14622574X-RAY DIFFRACTION100
1.799-1.88090.1761370.1462590X-RAY DIFFRACTION100
1.8809-1.980.16851360.14652596X-RAY DIFFRACTION100
1.98-2.10410.19061360.14512582X-RAY DIFFRACTION100
2.1041-2.26650.17351390.1482645X-RAY DIFFRACTION100
2.2665-2.49450.18581370.16712604X-RAY DIFFRACTION100
2.4945-2.85530.19891400.17822647X-RAY DIFFRACTION100
2.8553-3.59670.19871400.17382667X-RAY DIFFRACTION100
3.5967-32.8550.17571480.17182799X-RAY DIFFRACTION100

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