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- PDB-5fw6: Structure of human transthyretin mutant A108V -

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Basic information

Entry
Database: PDB / ID: 5fw6
TitleStructure of human transthyretin mutant A108V
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / TRASNPORT PROTEIN / T4-BINDING / T4-BINDING PROTEIN NON-AMYLOIDOGENIC
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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/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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGallego, P. / Varejao, N. / Santanna, R. / Saraiva, M.J. / Ventura, S. / Reverter, D.
CitationJournal: Sci Rep / Year: 2017
Title: Cavity filling mutations at the thyroxine-binding site dramatically increase transthyretin stability and prevent its aggregation.
Authors: Sant'Anna, R. / Almeida, M.R. / Varejao, N. / Gallego, P. / Esperante, S. / Ferreira, P. / Pereira-Henriques, A. / Palhano, F.L. / de Carvalho, M. / Foguel, D. / Reverter, D. / Saraiva, M.J. / Ventura, S.
History
DepositionFeb 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.2May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)27,6112
Polymers27,6112
Non-polymers00
Water3,207178
1
A: TRANSTHYRETIN

A: TRANSTHYRETIN

B: TRANSTHYRETIN

B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,2224
Polymers55,2224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_466x-1/2,-y+1,-z+3/21
crystal symmetry operation4_664-x+3/2,-y+1,z-1/21
Buried area6220 Å2
ΔGint-43.1 kcal/mol
Surface area19110 Å2
MethodPISA
2
B: TRANSTHYRETIN

B: TRANSTHYRETIN

A: TRANSTHYRETIN

A: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,2224
Polymers55,2224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
crystal symmetry operation3_566x+1/2,-y+1,-z+3/21
crystal symmetry operation4_665-x+3/2,-y+1,z+1/21
Buried area6220 Å2
ΔGint-43.1 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.692, 64.923, 85.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-2093-

HOH

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Components

#1: Protein TRANSTHYRETIN


Mass: 13805.414 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-147 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.68 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979493
DetectorType: RIGAKU CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 1.3→43.69 Å / Num. obs: 60275 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.9
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.3→64.92 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.347 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20294 3039 5 %RANDOM
Rwork0.16962 ---
obs0.17124 57155 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→64.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 178 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9492705
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41623.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57615301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.512158
X-RAY DIFFRACTIONr_chiral_restr0.1490.2305
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7081.51241
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.12122037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.873725
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.0674.5668
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.17831966
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 195 -
Rwork0.278 4078 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0584-0.3691-0.16560.61830.23840.77620.03340.1354-0.1496-0.03460.0363-0.00040.0987-0.0384-0.06970.0403-0.0077-0.01080.0368-0.02710.044620.20236.615929.6505
20.7517-0.1446-0.25260.41010.31430.8458-0.04230.1089-0.06380.00710.05580.00840.0696-0.008-0.01350.0242-0.00920.00820.0347-0.01470.024242.684438.861371.8915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 125
2X-RAY DIFFRACTION2B10 - 125

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