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- PDB-7dt8: Crystal structure of V30M mutated transthyretin in complex with 4... -

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Basic information

Entry
Database: PDB / ID: 7dt8
TitleCrystal structure of V30M mutated transthyretin in complex with 4-chloro-9-oxo-9H-xanthene-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-HH9 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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)35,3156
Polymers34,6852
Non-polymers6294
Water3,801211
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,62912
Polymers69,3704
Non-polymers1,2598
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6910 Å2
ΔGint-70 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.942, 85.839, 63.282
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-202-

HH9

21A-202-

HH9

31A-202-

HH9

41B-202-

HH9

51B-202-

HH9

61B-202-

HH9

71A-373-

HOH

81B-357-

HOH

91B-395-

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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HH9 / 4-chloranyl-9-oxidanylidene-xanthene-2-carboxylic acid


Mass: 274.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7ClO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 26.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, CaCl2, NaOAc

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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: 1.25→35.5 Å / Num. obs: 65385 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 17
Reflection shellResolution: 1.25→1.29 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6315 / CC1/2: 0.855 / Rpim(I) all: 0.232 / Rrim(I) all: 0.604

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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: 4pwe

4pwe


Resolution: 1.25→35.5 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 3267 5 %
Rwork0.1613 --
obs0.1621 65376 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 40 211 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051873
X-RAY DIFFRACTIONf_angle_d0.9012559
X-RAY DIFFRACTIONf_dihedral_angle_d19.001677
X-RAY DIFFRACTIONf_chiral_restr0.082284
X-RAY DIFFRACTIONf_plane_restr0.006321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2491-1.26770.25741340.19552533X-RAY DIFFRACTION95
1.2677-1.28750.20821390.18492650X-RAY DIFFRACTION99
1.2875-1.30860.21351400.17372655X-RAY DIFFRACTION100
1.3086-1.33120.231400.17532669X-RAY DIFFRACTION100
1.3312-1.35540.20241400.16732669X-RAY DIFFRACTION100
1.3554-1.38150.19391420.152692X-RAY DIFFRACTION100
1.3815-1.40970.14781390.14562657X-RAY DIFFRACTION100
1.4097-1.44030.16041420.13662693X-RAY DIFFRACTION100
1.4403-1.47380.15931410.13152687X-RAY DIFFRACTION100
1.4738-1.51070.14271410.13012674X-RAY DIFFRACTION100
1.5107-1.55150.1551420.12752687X-RAY DIFFRACTION100
1.5515-1.59720.16011400.132694X-RAY DIFFRACTION100
1.5972-1.64870.15661420.13152683X-RAY DIFFRACTION100
1.6487-1.70760.17131430.14262713X-RAY DIFFRACTION100
1.7076-1.7760.19521410.14952693X-RAY DIFFRACTION100
1.776-1.85680.18771420.14592698X-RAY DIFFRACTION100
1.8568-1.95470.15611430.1412715X-RAY DIFFRACTION100
1.9547-2.07720.14861430.14192706X-RAY DIFFRACTION100
2.0772-2.23760.16231440.14682741X-RAY DIFFRACTION100
2.2376-2.46270.1581440.16722738X-RAY DIFFRACTION100
2.4627-2.81890.17351460.17792767X-RAY DIFFRACTION100
2.8189-3.5510.19331460.17662785X-RAY DIFFRACTION100
3.551-35.5210.19171530.17552910X-RAY DIFFRACTION99

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