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- PDB-1fh2: TRANSTHYRETIN STABILITY AS A KEY FACTOR IN AMYLOIDOGENESIS -

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Basic information

Entry
Database: PDB / ID: 1fh2
TitleTRANSTHYRETIN STABILITY AS A KEY FACTOR IN AMYLOIDOGENESIS
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / Amyloid / Transthyretin / Protein Stability
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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/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 / Resolution: 1.8 Å
AuthorsSebastiao, M.P.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Transthyretin stability as a key factor in amyloidogenesis: X-ray analysis at atomic resolution.
Authors: Sebastiao, M.P. / Lamzin, V. / Saraiva, M.J. / Damas, A.M.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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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)27,6792
Polymers27,6792
Non-polymers00
Water1,76598
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,3584
Polymers55,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6360 Å2
ΔGint-55 kcal/mol
Surface area19160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.770, 86.310, 65.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer constructed from chains A and B by crystallographic two-fold symmetry.

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Components

#1: Protein TRANSTHYRETIN / PREALBUMIN / TBPA / TTR / ATTR


Mass: 13839.518 Da / Num. of mol.: 2 / Mutation: V30M/T119M / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: Ammonium Sulphate, Citrate Buffer, Glycerol, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal grow
*PLUS
pH: 5.3 / Method: vapor diffusion, hanging drop / Details: Damas, A.M., (1996) Acta Crystallog., D52, 966.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
241 %ammonium sulfate1reservoir
3200 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 121001 / Num. obs: 120772 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 5 % / Rmerge(I) obs: 0.318 / Num. unique all: 23677 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 23459 / % possible obs: 100 % / Num. measured all: 121001

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2128 1165 RANDOM
Rwork0.17 --
all0.1765 22140 -
obs0.1667 --
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 0 98 1892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.027
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS

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