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- PDB-8i0o: Crystal structure of Transthyretin variant A97S in monomeric form -

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Basic information

Entry
Database: PDB / ID: 8i0o
TitleCrystal structure of Transthyretin variant A97S in monomeric form
ComponentsTransthyretin
KeywordsSTRUCTURAL PROTEIN / Serum protein / amyloid / monomeric form / ATTR
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsAgrawal, S. / Yu, T.-Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)VTA112-V1-7-3 Taiwan
CitationJournal: To Be Published
Title: Structure and dynamics of Transthyretin pathogenic variant A97S
Authors: Agrawal, S. / Yu, T.-Y.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4186
Polymers55,1824
Non-polymers2362
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-77 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.932, 83.970, 84.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 13795.420 Da / Num. of mol.: 4 / Mutation: F87M, L110M, A97S
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 M Sodium HEPES; MOPS (acid), 0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide, 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 37066 / % possible obs: 93.97 % / Redundancy: 9.9 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.129 / Net I/σ(I): 16.23
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 3513 / Rpim(I) all: 0.324

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→25.79 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1814 5.02 %
Rwork0.1851 --
obs0.1875 36111 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 16 418 3982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013650
X-RAY DIFFRACTIONf_angle_d1.0794972
X-RAY DIFFRACTIONf_dihedral_angle_d13.9161292
X-RAY DIFFRACTIONf_chiral_restr0.07566
X-RAY DIFFRACTIONf_plane_restr0.009628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.3961140.32622141X-RAY DIFFRACTION77
1.93-1.990.23491250.23242276X-RAY DIFFRACTION83
1.99-2.050.24221220.19342477X-RAY DIFFRACTION89
2.05-2.130.22491300.20042504X-RAY DIFFRACTION90
2.13-2.210.24381390.19372538X-RAY DIFFRACTION92
2.21-2.310.38831420.27342607X-RAY DIFFRACTION94
2.31-2.430.22721430.18472732X-RAY DIFFRACTION98
2.43-2.590.25051430.18292772X-RAY DIFFRACTION99
2.59-2.790.23421490.17412790X-RAY DIFFRACTION100
2.79-3.070.26621470.17492812X-RAY DIFFRACTION100
3.07-3.510.19081520.1572831X-RAY DIFFRACTION100
3.51-4.420.18131520.14642872X-RAY DIFFRACTION100
4.42-25.790.21171560.18522945X-RAY DIFFRACTION99

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