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- PDB-8t5x: Probing the dissociation pathway of a kinetically labile transthy... -

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Basic information

Entry
Database: PDB / ID: 8t5x
TitleProbing the dissociation pathway of a kinetically labile transthyretin mutant (A25T)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Aggregation / Amyloid
Function / homology
Function and homology information


thyroid hormone binding / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space
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: 1.63 Å
AuthorsFerguson, J.A. / Sun, X. / Leach, B.I. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DK34909 United States
American Heart Association20POST35050060 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Probing the Dissociation Pathway of a Kinetically Labile Transthyretin Mutant.
Authors: Sun, X. / Ferguson, J.A. / Leach, B.I. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionJun 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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)27,6152
Polymers27,6152
Non-polymers00
Water3,369187
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


  • defined by author&software
  • Evidence: homology, Protein is a tetramer in solution as shown extensively by the literature. Often the P21212 space groups have a symmetry axis that goes down the strong dimer interface as as the ...Evidence: homology, Protein is a tetramer in solution as shown extensively by the literature. Often the P21212 space groups have a symmetry axis that goes down the strong dimer interface as as the case here. As such the Asymmetric unit here is what the literature calls the tight dimer.
  • 55.2 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)55,2304
Polymers55,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6060 Å2
ΔGint-45 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.780, 86.030, 64.652
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-259-

HOH

21B-245-

HOH

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Components

#1: Protein Transthyretin


Mass: 13807.387 Da / Num. of mol.: 2 / Mutation: A25T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, HEL111, hCG_25470 / Variant: A25T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9KL36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: In drop 1:1 mixture of sample buffer and crystal condition Buffer :10mg/ml protein, 10 mM phosphate potassium, 100 mM KCl at pH 7.0 Crystal Condition: 0.1 M sodium cacodylate (pH 6.5), 0.2 M ...Details: In drop 1:1 mixture of sample buffer and crystal condition Buffer :10mg/ml protein, 10 mM phosphate potassium, 100 mM KCl at pH 7.0 Crystal Condition: 0.1 M sodium cacodylate (pH 6.5), 0.2 M calcium acetate and 40 % (w/v) PEG 300 at 277 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.63→39.02 Å / Num. obs: 30727 / % possible obs: 98.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 18.07 Å2 / CC1/2: 0.871 / Rpim(I) all: 0.04 / Rrim(I) all: 0.115 / Net I/σ(I): 22.2
Reflection shellResolution: 1.63→1.68 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1544 / CC1/2: 0.415 / Rpim(I) all: 0.705 / Rrim(I) all: 1.91 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.20.1_4487refinement
Cootmodel building
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→39.02 Å / SU ML: 0.194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 1541 5.03 %
Rwork0.1882 29096 -
obs0.1904 30637 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.45 Å2
Refinement stepCycle: LAST / Resolution: 1.63→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 187 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01031901
X-RAY DIFFRACTIONf_angle_d1.12152613
X-RAY DIFFRACTIONf_chiral_restr0.0642299
X-RAY DIFFRACTIONf_plane_restr0.0254337
X-RAY DIFFRACTIONf_dihedral_angle_d7.1225268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.34751090.30392510X-RAY DIFFRACTION94.31
1.68-1.740.32681380.2882561X-RAY DIFFRACTION97.58
1.74-1.810.3241370.27472613X-RAY DIFFRACTION98.21
1.81-1.90.2961330.23312610X-RAY DIFFRACTION98.28
1.9-20.21181340.20262617X-RAY DIFFRACTION98.81
2-2.120.20891440.18092630X-RAY DIFFRACTION98.75
2.12-2.290.22191480.18452640X-RAY DIFFRACTION99.18
2.29-2.520.22571670.17952635X-RAY DIFFRACTION99.15
2.52-2.880.21051470.17712681X-RAY DIFFRACTION99.51
2.88-3.630.24811380.16862744X-RAY DIFFRACTION99.72
3.63-39.020.20681460.16372855X-RAY DIFFRACTION99.5

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