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- PDB-1f86: TRANSTHYRETIN THR119MET PROTEIN STABILISATION -

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Basic information

Entry
Database: PDB / ID: 1f86
TitleTRANSTHYRETIN THR119MET PROTEIN STABILISATION
ComponentsTRANSTHYRETIN THR119MET VARIANT
KeywordsTRANSPORT PROTEIN / transthyretin / protein stability / X-ray crystal structure / amyloidogenesis
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
3,5,3',5'-TETRAIODO-L-THYRONINE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / WILD-TYPE TTR (1TTA) / Resolution: 1.1 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
DepositionJun 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Advisory / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN THR119MET VARIANT
B: TRANSTHYRETIN THR119MET VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8264
Polymers25,2722
Non-polymers1,5542
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-13 kcal/mol
Surface area11370 Å2
MethodPISA
2
A: TRANSTHYRETIN THR119MET VARIANT
B: TRANSTHYRETIN THR119MET VARIANT
hetero molecules

A: TRANSTHYRETIN THR119MET VARIANT
B: TRANSTHYRETIN THR119MET VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6528
Polymers50,5454
Non-polymers3,1074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9140 Å2
ΔGint-45 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.680, 85.770, 63.690
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 and a symmetry partner generated by a two-fold axis.

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Components

#1: Protein TRANSTHYRETIN THR119MET VARIANT


Mass: 12636.194 Da / Num. of mol.: 2 / Mutation: THR119MET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pINTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: sodium citrate, 1,2,3 heptanetriol, ammonium sulphate, glycerol, methanol, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. all: 95607 / Num. obs: 1561421 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.1
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 7 % / Rmerge(I) obs: 0.497 / % possible all: 95.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 95607 / Num. measured all: 1561421

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: WILD-TYPE TTR (1TTA) / Resolution: 1.1→5 Å / Num. parameters: 20555 / Num. restraintsaints: 25205 / Isotropic thermal model: MOLECULAR REPLACEMENT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.177 9278 5 %RANDOM
Rwork0.147 ---
obs0.14 ---
all-73289 --
Solvent computationSolvent model: MOEWS&KRETSINGER, J.MOL.BOL.91(1973)201-228
Refine analyzeNum. disordered residues: 34 / Occupancy sum hydrogen: 0
Refinement stepCycle: LAST / Resolution: 1.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 38 253 2184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.088
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor all: 0.14 / Rfactor obs: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS

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