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- PDB-6fxu: Crystal structure of human transthyretin mutant T119M at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6fxu
TitleCrystal structure of human transthyretin mutant T119M at pH 5.5
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloid / Gatekeeper / Aggregation / Stability
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: 1.359 Å
AuthorsVarejao, N. / Esperante, S. / Ventura, S. / Reverter, D.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation.
Authors: Esperante, S.A. / Varejao, N. / Pinheiro, F. / Sant'Anna, R. / Luque-Ortega, J.R. / Alfonso, C. / Sora, V. / Papaleo, E. / Rivas, G. / Reverter, D. / Ventura, S.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
Water3,261181
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,2304
Polymers55,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area6380 Å2
ΔGint-51 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.075, 43.183, 63.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-280-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13807.452 Da / Num. of mol.: 2 / Mutation: T119M
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.: 181 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 7% glycerol, 1.3 M sodium citrate, pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.359→63.834 Å / Num. obs: 46691 / % possible obs: 89.8 % / Redundancy: 7.5 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.017 / Rrim(I) all: 0.045 / Net I/σ(I): 22.4 / Num. measured all: 350886
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.359-1.3646.61.03132584930.5950.4381.123295.4
6.307-63.8346.70.02441366130.9990.0110.02665.3100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASER1.7.3-928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.359→63.834 Å / FOM work R set: 0.8155 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2272 4.87 %
Rwork0.1919 44367 -
obs0.1931 46639 89.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.19 Å2 / Biso mean: 22.85 Å2 / Biso min: 8.39 Å2
Refinement stepCycle: final / Resolution: 1.359→63.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 0 181 1964
Biso mean---34.8 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071881
X-RAY DIFFRACTIONf_angle_d1.082572
X-RAY DIFFRACTIONf_chiral_restr0.045289
X-RAY DIFFRACTIONf_plane_restr0.007332
X-RAY DIFFRACTIONf_dihedral_angle_d14.515668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3592-1.38880.36951370.3513064320199
1.3888-1.42110.28421560.307429903146100
1.4211-1.45660.32461580.281630683226100
1.4566-1.4960.27161270.253630713198100
1.496-1.540.25821470.234830823229100
1.54-1.58970.22751860.201829833169100
1.5897-1.64660.17831440.185830893233100
1.6466-1.71250.20181550.184530623217100
1.7125-1.79040.21611480.19192630277885
1.7904-1.88480.19871360.18772764290089
1.8848-2.00290.209850.17541815190059
2.0029-2.15760.2155740.1811361143544
2.1576-2.37470.19641570.17512716287388
2.3747-2.71840.22981360.19642496263280
2.7184-3.42480.22721580.193131143272100
3.4248-63.90450.19621680.16853062323095
Refinement TLS params.Method: refined / Origin x: -13.0305 Å / Origin y: -22.7454 Å / Origin z: -15.7727 Å
111213212223313233
T0.0876 Å2-0.0074 Å2-0.002 Å2-0.0899 Å2-0.0001 Å2--0.1078 Å2
L1.006 °20.0523 °20.0121 °2-0.7 °20.1064 °2--0.812 °2
S-0.0363 Å °0.0945 Å °-0.0144 Å °-0.0422 Å °-0.0164 Å °0.1137 Å °-0.036 Å °-0.0059 Å °0.0468 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 125
2X-RAY DIFFRACTION1allB10 - 125
3X-RAY DIFFRACTION1allS1 - 188

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