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- PDB-8hy4: Crystal structure of human transthyretin variant A97S at pH 7.6 -

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Basic information

Entry
Database: PDB / ID: 8hy4
TitleCrystal structure of human transthyretin variant A97S at pH 7.6
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transport thyroxine
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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: 1.53 Å
AuthorsWang, Y.S. / Huang, C.H. / Tzeng, S.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2023
Title: A molecular basis for tetramer destabilization and aggregation of transthyretin Ala97Ser.
Authors: Wang, Y.S. / Huang, C.H. / Liou, G.G. / Hsueh, H.W. / Liang, C.T. / Tseng, H.C. / Huang, S.J. / Chao, C.C. / Hsieh, S.T. / Tzeng, S.R.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)29,9912
Polymers29,9912
Non-polymers00
Water2,486138
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)59,9834
Polymers59,9834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6250 Å2
ΔGint-46 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.370, 41.272, 63.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

21A-257-

HOH

31B-235-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14995.710 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 (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.87 Å3/Da / Density % sol: 34.23 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES, pH 7.6, 38% PEG 400, and 0.4 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. obs: 34570 / % possible obs: 99.39 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 29.912698412698
Reflection shellResolution: 1.53→1.58 Å / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.0327868852459 / Num. unique obs: 3382 / Rpim(I) all: 0.34 / Rrim(I) all: 0.84

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→21.99 Å / SU ML: 0.1698 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2566 1999 5.78 %
Rwork0.2208 32570 -
obs0.2228 34569 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.85 Å2
Refinement stepCycle: LAST / Resolution: 1.53→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 0 138 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631809
X-RAY DIFFRACTIONf_angle_d0.92462468
X-RAY DIFFRACTIONf_chiral_restr0.0652284
X-RAY DIFFRACTIONf_plane_restr0.0093310
X-RAY DIFFRACTIONf_dihedral_angle_d15.8825637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.3381330.28042165X-RAY DIFFRACTION95.35
1.57-1.610.28881410.26062305X-RAY DIFFRACTION99.39
1.61-1.660.26991410.24312297X-RAY DIFFRACTION99.84
1.66-1.710.30011410.22662292X-RAY DIFFRACTION99.88
1.71-1.770.27481430.24042319X-RAY DIFFRACTION99.76
1.77-1.840.2641410.21972295X-RAY DIFFRACTION100
1.84-1.930.23551420.20992318X-RAY DIFFRACTION99.84
1.93-2.030.24151420.20712311X-RAY DIFFRACTION99.96
2.03-2.150.25491440.20062335X-RAY DIFFRACTION99.92
2.15-2.320.25811440.20692351X-RAY DIFFRACTION100
2.32-2.550.27521430.22822344X-RAY DIFFRACTION99.84
2.55-2.920.24691440.22672360X-RAY DIFFRACTION99.68
2.92-3.680.25631460.2142382X-RAY DIFFRACTION99.61
3.68-21.990.24641540.22312496X-RAY DIFFRACTION99.07

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