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- PDB-5fo2: Structure of human transthyretin mutant A108I -

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Basic information

Entry
Database: PDB / ID: 5fo2
TitleStructure of human transthyretin mutant A108I
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / T4-BINDING PROTEIN NON-AMYLOIDOGENIC
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/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 / OTHER / Resolution: 1.449 Å
AuthorsVarejao, N. / Santanna, R. / Saraiva, M.J. / Gallego, P. / 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
DepositionNov 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: 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 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)27,6392
Polymers27,6392
Non-polymers00
Water4,900272
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,2784
Polymers55,2784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area6380 Å2
ΔGint-44.6 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.255, 43.586, 64.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 13819.440 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 / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.18 Å3/Da / Density % sol: 43.63 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 28% PEG400, 0.2M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.3
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.45→85.2 Å / Num. obs: 42899 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 1.44→1.45 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.449→64.919 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 2103 4.9 %
Rwork0.1837 --
obs0.1852 42865 97.97 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.155 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9251 Å20 Å20 Å2
2--2.783 Å20 Å2
3---0.1421 Å2
Refinement stepCycle: LAST / Resolution: 1.449→64.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 0 272 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181868
X-RAY DIFFRACTIONf_angle_d1.7542555
X-RAY DIFFRACTIONf_dihedral_angle_d13.682667
X-RAY DIFFRACTIONf_chiral_restr0.119293
X-RAY DIFFRACTIONf_plane_restr0.012324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4489-1.48260.35421360.31732557X-RAY DIFFRACTION95
1.4826-1.51970.31291290.27172665X-RAY DIFFRACTION97
1.5197-1.56080.25681220.23182694X-RAY DIFFRACTION97
1.5608-1.60670.27841380.222647X-RAY DIFFRACTION97
1.6067-1.65860.23621460.19652658X-RAY DIFFRACTION98
1.6586-1.71790.24941570.20232659X-RAY DIFFRACTION98
1.7179-1.78670.23891130.18682722X-RAY DIFFRACTION98
1.7867-1.8680.19091740.17082675X-RAY DIFFRACTION98
1.868-1.96650.18351400.16092720X-RAY DIFFRACTION98
1.9665-2.08970.20781510.16562713X-RAY DIFFRACTION98
2.0897-2.2510.19581350.16682727X-RAY DIFFRACTION99
2.251-2.47760.23511210.17492782X-RAY DIFFRACTION99
2.4776-2.83610.23721390.18352781X-RAY DIFFRACTION99
2.8361-3.57310.20091540.17562805X-RAY DIFFRACTION99
3.5731-64.98420.20081480.18542957X-RAY DIFFRACTION99
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)
11.3445-0.4305-0.69111.54570.41311.1929-0.01760.1022-0.0147-0.0274-0.0543-0.13970.00790.04280.06460.08580.0050.00590.10540.01060.097513.080644.137571.1057
21.65270.23580.19941.62030.22071.3937-0.0762-0.25270.01710.19230.0266-0.2582-0.06950.13380.05230.15460.0347-0.0340.17630.00570.135812.822341.988791.056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ -10:9999)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ -10:9999)

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