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- PDB-7dt6: Crystal structure of V30M mutated transthyretin in complex with p... -

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Basic information

Entry
Database: PDB / ID: 7dt6
TitleCrystal structure of V30M mutated transthyretin in complex with purpurin
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
Purpurin / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)34,9413
Polymers34,6852
Non-polymers2561
Water4,179232
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8836
Polymers69,3704
Non-polymers5122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)42.930, 85.430, 63.690
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-271-

HOH

21B-364-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17342.582 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-9TF / Purpurin


Mass: 256.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.68 Å3/Da / Density % sol: 26.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, CaC2l, NaOAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→42.9 Å / Num. obs: 56091 / % possible obs: 96 % / Redundancy: 6.3 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Net I/σ(I): 15.5
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5685 / Rpim(I) all: 0.492 / Rrim(I) all: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pwe

4pwe


Resolution: 1.3→30.28 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 2802 5 %
Rwork0.1871 --
obs0.1882 56067 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 19 232 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061872
X-RAY DIFFRACTIONf_angle_d0.8932560
X-RAY DIFFRACTIONf_dihedral_angle_d19.959658
X-RAY DIFFRACTIONf_chiral_restr0.097287
X-RAY DIFFRACTIONf_plane_restr0.009322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.32250.30111400.30872667X-RAY DIFFRACTION99
1.3225-1.34650.29771440.29622732X-RAY DIFFRACTION99
1.3465-1.37240.2741420.27512683X-RAY DIFFRACTION99
1.3724-1.40040.3321420.26922705X-RAY DIFFRACTION99
1.4004-1.43090.2961420.26172706X-RAY DIFFRACTION99
1.4309-1.46420.26871410.24472677X-RAY DIFFRACTION98
1.4642-1.50080.24371420.2342685X-RAY DIFFRACTION98
1.5008-1.54140.2431420.21762702X-RAY DIFFRACTION98
1.5414-1.58670.25031410.2192681X-RAY DIFFRACTION97
1.5867-1.63790.2331420.20452691X-RAY DIFFRACTION98
1.6379-1.69650.23681390.20542653X-RAY DIFFRACTION97
1.6965-1.76440.21671400.20952658X-RAY DIFFRACTION96
1.7644-1.84470.21031400.19752663X-RAY DIFFRACTION96
1.8447-1.94190.21231400.18012660X-RAY DIFFRACTION95
1.9419-2.06360.181380.1712622X-RAY DIFFRACTION95
2.0636-2.22280.17691390.16882642X-RAY DIFFRACTION95
2.2228-2.44650.22121380.17922626X-RAY DIFFRACTION94
2.4465-2.80020.19531360.18152605X-RAY DIFFRACTION93
2.8002-3.52720.22361360.17272589X-RAY DIFFRACTION91
3.5272-30.280.18351380.16452618X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -22.6458 Å / Origin y: 13.0601 Å / Origin z: -15.8112 Å
111213212223313233
T0.1086 Å20.0023 Å20.0126 Å2-0.1298 Å20.0037 Å2--0.1306 Å2
L0.562 °2-0.0457 °20.1791 °2-0.7947 °20.0343 °2--0.911 °2
S-0.0297 Å °0.0202 Å °0.0972 Å °-0.0256 Å °-0.0193 Å °-0.0075 Å °-0.0191 Å °0.0441 Å °0.0469 Å °
Refinement TLS groupSelection details: not water and not resname PDB

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