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- PDB-5oq0: Crystal structure of transthyretin mutant 87-110-117 -

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Basic information

Entry
Database: PDB / ID: 5oq0
TitleCrystal structure of transthyretin mutant 87-110-117
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis / homo-tetramer / retinol-binding protein / TTR
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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: 1.94 Å
AuthorsZanotti, G. / Vallese, F. / Berni, R.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural and dynamics evidence for scaffold asymmetric flexibility of the human transthyretin tetramer.
Authors: Zanotti, G. / Vallese, F. / Ferrari, A. / Menozzi, I. / Saldano, T.E. / Berto, P. / Fernandez-Alberti, S. / Berni, R.
History
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin


Theoretical massNumber of molelcules
Total (without water)13,8211
Polymers13,8211
Non-polymers00
Water48627
1
A: Transthyretin

A: Transthyretin

A: Transthyretin

A: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,2864
Polymers55,2864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-x+2,-y+3,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_585x,-y+3,-z1
Buried area6220 Å2
ΔGint-52 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.249, 67.044, 83.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 13821.456 Da / Num. of mol.: 1 / Mutation: F87M/L110M/S117E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium phosphate (pH 7.5), 2.2 M ammonium sulphate
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973186 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973186 Å / Relative weight: 1
ReflectionResolution: 1.94→52.29 Å / Num. obs: 9125 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Net I/σ(I): 13
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 1.6 / Rpim(I) all: 0.514 / % possible all: 80.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WO0

4wo0


Resolution: 1.94→41.783 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.57
RfactorNum. reflection% reflection
Rfree0.2671 428 4.84 %
Rwork0.2278 --
obs0.2296 8841 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→41.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 0 27 923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008919
X-RAY DIFFRACTIONf_angle_d0.9441253
X-RAY DIFFRACTIONf_dihedral_angle_d14.077545
X-RAY DIFFRACTIONf_chiral_restr0.06142
X-RAY DIFFRACTIONf_plane_restr0.009160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.22070.32511410.29322586X-RAY DIFFRACTION91
2.2207-2.79780.3071430.30242846X-RAY DIFFRACTION99
2.7978-41.79270.24611440.19862981X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.0719 Å / Origin y: 90.1711 Å / Origin z: 12.8608 Å
111213212223313233
T0.285 Å2-0.0163 Å20.0265 Å2-0.2757 Å2-0.0132 Å2--0.2749 Å2
L1.303 °20.0274 °2-0.9754 °2-1.3647 °2-0.4242 °2--2.9259 °2
S0.095 Å °-0.5812 Å °0.1439 Å °-0.0137 Å °0.046 Å °-0.0188 Å °-0.2621 Å °0.3106 Å °0.0023 Å °
Refinement TLS groupSelection details: all

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