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- PDB-7dt3: Crystal structure of human transthyretin in complex with 4-chloro... -

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Basic information

Entry
Database: PDB / ID: 7dt3
TitleCrystal structure of human transthyretin in complex with 4-chloro-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Inhibitor / Complex / T4-binding / amyloidosis
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 / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...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 / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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-HG6 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.198 Å
AuthorsKitakami, R. / Yokoyama, T. / Mizuguchi, M.
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Inhibitory activities of anthraquinone and xanthone derivatives against transthyretin amyloidogenesis.
Authors: Kitakami, R. / Inui, K. / Nakagawa, Y. / Sawai, Y. / Katayama, W. / Yokoyama, T. / Okada, T. / Kanamitsu, K. / Nakagawa, S. / Toyooka, N. / Mizuguchi, M.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2756
Polymers34,6212
Non-polymers6534
Water3,729207
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54912
Polymers69,2424
Non-polymers1,3078
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)42.029, 85.773, 63.708
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-363-

HOH

21B-356-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17310.518 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 (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HG6 / 4-chloranyl-9,10-bis(oxidanylidene)anthracene-2-carboxylic acid


Mass: 286.667 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H7ClO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.66 Å3/Da / Density % sol: 25.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG400, 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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.198→42.89 Å / Num. obs: 71443 / % possible obs: 97.8 % / Redundancy: 6.3 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 16.3
Reflection shellResolution: 1.198→1.24 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5753 / Rpim(I) all: 0.301 / Rrim(I) all: 0.668

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Processing

Software
NameVersionClassification
PHENIX(1.12-2829_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N85

4n85


Resolution: 1.198→31.854 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 3573 5 %
Rwork0.1656 --
obs0.1666 71436 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.198→31.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 42 207 2017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051937
X-RAY DIFFRACTIONf_angle_d0.8462669
X-RAY DIFFRACTIONf_dihedral_angle_d22.431692
X-RAY DIFFRACTIONf_chiral_restr0.082297
X-RAY DIFFRACTIONf_plane_restr0.007341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1982-1.21390.22021010.21916X-RAY DIFFRACTION73
1.2139-1.23060.23691130.19512148X-RAY DIFFRACTION81
1.2306-1.24810.1771240.18192356X-RAY DIFFRACTION89
1.2481-1.26680.21131360.1682573X-RAY DIFFRACTION98
1.2668-1.28660.19951390.16052651X-RAY DIFFRACTION100
1.2866-1.30770.18421390.16112643X-RAY DIFFRACTION100
1.3077-1.33020.19081390.15562623X-RAY DIFFRACTION100
1.3302-1.35440.19191390.15042656X-RAY DIFFRACTION100
1.3544-1.38050.1721390.13862627X-RAY DIFFRACTION100
1.3805-1.40860.18161390.14072653X-RAY DIFFRACTION100
1.4086-1.43930.16651390.13452631X-RAY DIFFRACTION100
1.4393-1.47270.17191390.1392654X-RAY DIFFRACTION100
1.4727-1.50960.17721400.13952655X-RAY DIFFRACTION100
1.5096-1.55040.15631400.13332658X-RAY DIFFRACTION100
1.5504-1.5960.15811390.13742647X-RAY DIFFRACTION100
1.596-1.64750.17781410.13552668X-RAY DIFFRACTION100
1.6475-1.70640.171390.15212642X-RAY DIFFRACTION100
1.7064-1.77470.18511410.1542684X-RAY DIFFRACTION100
1.7747-1.85550.15921400.15472662X-RAY DIFFRACTION100
1.8555-1.95330.17191410.15042681X-RAY DIFFRACTION100
1.9533-2.07560.16141420.15572683X-RAY DIFFRACTION100
2.0756-2.23590.17191420.14952701X-RAY DIFFRACTION100
2.2359-2.46080.18291420.17092707X-RAY DIFFRACTION100
2.4608-2.81670.20271430.19162719X-RAY DIFFRACTION100
2.8167-3.5480.19671450.18282748X-RAY DIFFRACTION100
3.548-31.8540.20611520.1782877X-RAY DIFFRACTION100

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