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- PDB-7ejq: Crystal structure of human transthyretin in complex with 8-chloro... -

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Basic information

Entry
Database: PDB / ID: 7ejq
TitleCrystal structure of human 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: 1.15 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)34,9926
Polymers34,3632
Non-polymers6294
Water3,747208
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)42.027, 85.359, 63.487
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
11B-202-

J5R

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17181.404 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.: 208 / 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: 25.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 1.15→42.68 Å / Num. obs: 79314 / % possible obs: 96.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Net I/σ(I): 23.5
Reflection shellResolution: 1.15→1.19 Å / Mean I/σ(I) obs: 6.2 / Num. unique obs: 7242 / CC1/2: 0.971 / Rpim(I) all: 0.114 / Rrim(I) all: 0.293

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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: 1.15→29.946 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 3963 5 %
Rwork0.1447 --
obs0.1458 79296 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→29.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 40 208 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071912
X-RAY DIFFRACTIONf_angle_d1.0312625
X-RAY DIFFRACTIONf_dihedral_angle_d22.946702
X-RAY DIFFRACTIONf_chiral_restr0.085293
X-RAY DIFFRACTIONf_plane_restr0.008336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.149-1.1630.1721210.13382290X-RAY DIFFRACTION83
1.163-1.17770.15221340.12752546X-RAY DIFFRACTION92
1.1777-1.19320.14671360.12342599X-RAY DIFFRACTION94
1.1932-1.20960.1411380.12242623X-RAY DIFFRACTION95
1.2096-1.22690.19571370.1242614X-RAY DIFFRACTION95
1.2269-1.24520.13971380.122625X-RAY DIFFRACTION95
1.2452-1.26460.13581400.11662656X-RAY DIFFRACTION96
1.2646-1.28540.15631390.11892630X-RAY DIFFRACTION96
1.2854-1.30750.15731390.11922645X-RAY DIFFRACTION96
1.3075-1.33130.1471410.122675X-RAY DIFFRACTION96
1.3313-1.35690.13381400.11822664X-RAY DIFFRACTION96
1.3569-1.38460.13361400.11332667X-RAY DIFFRACTION96
1.3846-1.41470.13011390.11712646X-RAY DIFFRACTION97
1.4147-1.44760.13871430.12112726X-RAY DIFFRACTION97
1.4476-1.48380.14621400.12162663X-RAY DIFFRACTION97
1.4838-1.5240.15671430.1212716X-RAY DIFFRACTION98
1.524-1.56880.15921420.12332702X-RAY DIFFRACTION98
1.5688-1.61940.14151450.12012741X-RAY DIFFRACTION98
1.6194-1.67730.15591420.12952701X-RAY DIFFRACTION98
1.6773-1.74450.14851450.13292751X-RAY DIFFRACTION98
1.7445-1.82380.14271430.13992725X-RAY DIFFRACTION98
1.8238-1.920.13851440.13032729X-RAY DIFFRACTION98
1.92-2.04030.14961450.13182769X-RAY DIFFRACTION99
2.0403-2.19770.14391480.12992798X-RAY DIFFRACTION99
2.1977-2.41880.16791460.14522790X-RAY DIFFRACTION99
2.4188-2.76860.17081490.16542828X-RAY DIFFRACTION99
2.7686-3.48730.1811500.1662838X-RAY DIFFRACTION99
3.4873-29.9460.21811560.17182976X-RAY DIFFRACTION99

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