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- PDB-7ejr: Crystal structure of V30M mutated transthyretin in complex with 8... -

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Basic information

Entry
Database: PDB / ID: 7ejr
TitleCrystal structure of V30M mutated transthyretin in complex with 8-chloro-9-oxo-9H-xanthene-3-carboxylic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloidosis / inhibitor / complex
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
Chem-J5R / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 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
DepositionApr 2, 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)35,0566
Polymers34,4272
Non-polymers6294
Water3,153175
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)42.139, 85.929, 62.858
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-

J5R

21B-202-

J5R

31B-304-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17213.469 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-J5R / 8-chloranyl-9-oxidanylidene-xanthene-3-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.: 175 / 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: 1.65 Å3/Da / Density % sol: 25.58 %
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 PILATUS 6M / 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: 1.45→35.47 Å / Num. obs: 41002 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Net I/σ(I): 21
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3921 / CC1/2: 0.915 / Rpim(I) all: 0.192 / Rrim(I) all: 0.497

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N85

4n85


Resolution: 1.451→31.429 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 2050 5 %
Rwork0.1938 --
obs0.1944 41002 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→31.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 40 175 1995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061908
X-RAY DIFFRACTIONf_angle_d0.9412615
X-RAY DIFFRACTIONf_dihedral_angle_d22.423702
X-RAY DIFFRACTIONf_chiral_restr0.084290
X-RAY DIFFRACTIONf_plane_restr0.006334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.451-1.48480.25161290.23742447X-RAY DIFFRACTION96
1.4848-1.52190.23281350.21812562X-RAY DIFFRACTION100
1.5219-1.5630.21921360.21142584X-RAY DIFFRACTION100
1.563-1.6090.23981350.19952559X-RAY DIFFRACTION100
1.609-1.6610.23181350.19922565X-RAY DIFFRACTION100
1.661-1.72030.23491360.2022589X-RAY DIFFRACTION100
1.7203-1.78920.22841350.21382568X-RAY DIFFRACTION100
1.7892-1.87060.23581350.20082574X-RAY DIFFRACTION100
1.8706-1.96920.20261370.19222594X-RAY DIFFRACTION100
1.9692-2.09260.17961380.19062618X-RAY DIFFRACTION100
2.0926-2.25410.21031360.18922578X-RAY DIFFRACTION100
2.2541-2.48090.21741380.19752624X-RAY DIFFRACTION100
2.4809-2.83960.22521380.19842634X-RAY DIFFRACTION100
2.8396-3.57690.18481410.19432670X-RAY DIFFRACTION100
3.5769-31.4290.20081460.18292786X-RAY DIFFRACTION100

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