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- PDB-7y6j: Crystal structure of human transthyretin variant A97S at pH 5.4 -

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Basic information

Entry
Database: PDB / ID: 7y6j
TitleCrystal structure of human transthyretin variant A97S at pH 5.4
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transport thyroxine
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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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
DepositionJun 20, 2022Deposition 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9556
Polymers27,5872
Non-polymers3684
Water3,747208
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91012
Polymers55,1734
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6790 Å2
ΔGint-42 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.405, 42.455, 64.851
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-320-

HOH

21B-339-

HOH

31B-400-

HOH

41B-402-

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 (E. coli) / References: UniProt: P02766
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.75 M Ammonium sulfate, 0.01 M Citrate buffer, pH 5.4

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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 315r / Detector: CCD / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 52718 / % possible obs: 99.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.87 Å2 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.016 / Rrim(I) all: 0.034 / Net I/σ(I): 42.88
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.058 / Num. unique obs: 4890 / Rpim(I) all: 0.283 / Rrim(I) all: 0.552 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
HKL-2000data scaling
PHENIX1.18.2_3874phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.38→22.13 Å / SU ML: 0.1141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1911 1886 3.8 %
Rwork0.1502 47791 -
obs0.1518 49677 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.92 Å2
Refinement stepCycle: LAST / Resolution: 1.38→22.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 24 208 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481843
X-RAY DIFFRACTIONf_angle_d0.82932511
X-RAY DIFFRACTIONf_chiral_restr0.0813287
X-RAY DIFFRACTIONf_plane_restr0.0073315
X-RAY DIFFRACTIONf_dihedral_angle_d7.5729257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.24161420.19273597X-RAY DIFFRACTION99.05
1.42-1.460.21021430.16543629X-RAY DIFFRACTION99.97
1.46-1.510.19651430.15513630X-RAY DIFFRACTION99.97
1.51-1.560.1721440.14443618X-RAY DIFFRACTION99.95
1.56-1.620.19491430.13143656X-RAY DIFFRACTION99.97
1.62-1.70.1731450.13443667X-RAY DIFFRACTION99.97
1.7-1.790.16071430.13583640X-RAY DIFFRACTION99.89
1.79-1.90.1721450.13143669X-RAY DIFFRACTION99.9
1.9-2.040.16221460.12813682X-RAY DIFFRACTION99.97
2.04-2.250.16911450.13393686X-RAY DIFFRACTION99.77
2.25-2.570.18411460.1573698X-RAY DIFFRACTION99.61
2.57-3.240.17791480.16353758X-RAY DIFFRACTION99.69
3.24-22.130.22871530.15863861X-RAY DIFFRACTION98.41

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