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- PDB-8i00: Crystal structure of A97S transthyretin -

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Basic information

Entry
Database: PDB / ID: 8i00
TitleCrystal structure of A97S transthyretin
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / Amyloid / Transporter / Serum protein / Tetramer
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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: 1.8 Å
AuthorsAgrawal, S. / Yu, T.-Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-VTA-112-13 Taiwan
CitationJournal: To Be Published
Title: Structure and dynamics of pathogenic transthyretin variant A97S
Authors: Agrawal, S. / Yu, T.-Y.
History
DepositionJan 10, 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


Theoretical massNumber of molelcules
Total (without water)27,5872
Polymers27,5872
Non-polymers00
Water3,639202
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,1734
Polymers55,1734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6220 Å2
ΔGint-43 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.630, 43.092, 64.058
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-259-

HOH

21A-293-

HOH

31B-266-

HOH

41B-302-

HOH

51B-305-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13793.360 Da / Num. of mol.: 2 / Mutation: A97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Sodium citrate tribasic dihydrate

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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: 1.8→50 Å / Num. obs: 22653 / % possible obs: 97.47 % / Redundancy: 6.7 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.038 / Net I/σ(I): 41.77
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 2197 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.07 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 2000 9.06 %
Rwork0.1798 --
obs0.1824 22067 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→26.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 202 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061789
X-RAY DIFFRACTIONf_angle_d0.7462439
X-RAY DIFFRACTIONf_dihedral_angle_d12.906627
X-RAY DIFFRACTIONf_chiral_restr0.061280
X-RAY DIFFRACTIONf_plane_restr0.007307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.28381400.21891398X-RAY DIFFRACTION98
1.85-1.90.20951430.17341440X-RAY DIFFRACTION99
1.9-1.950.19621440.16811451X-RAY DIFFRACTION100
1.95-2.010.22291410.15871406X-RAY DIFFRACTION99
2.01-2.090.1881450.16181456X-RAY DIFFRACTION100
2.09-2.170.18981440.15231442X-RAY DIFFRACTION100
2.17-2.270.20371450.16091466X-RAY DIFFRACTION100
2.27-2.390.18971450.16471449X-RAY DIFFRACTION100
2.39-2.540.21441460.16581458X-RAY DIFFRACTION100
2.54-2.730.19631440.17421454X-RAY DIFFRACTION100
2.73-3.010.21091460.17431471X-RAY DIFFRACTION100
3.01-3.440.19981480.181468X-RAY DIFFRACTION98
3.44-4.330.20971340.18151355X-RAY DIFFRACTION90
4.33-26.070.23171350.2361353X-RAY DIFFRACTION85

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