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- PDB-6e78: Structure of Human Transthyretin Asp38Ala Mutant in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+78
TitleStructure of Human Transthyretin Asp38Ala Mutant in Complex with Diflunisal
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / diflunisal
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, 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
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.499 Å
AuthorsChung, K. / Saelices, L. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG048120 United States
CitationJournal: To Be Published
Title: Structural Variants of Transthyretin
Authors: Saelices, L. / Chung, K. / Esswein, S. / Chou, J. / Liang, W. / Li, J.H. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7214
Polymers25,2202
Non-polymers5002
Water1,40578
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4418
Polymers50,4404
Non-polymers1,0014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8500 Å2
ΔGint-53 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.210, 85.440, 64.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

1FL

21B-201-

1FL

31B-201-

1FL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 12 or resid 14...
21(chain B and (resid 10 through 12 or resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 10 through 12 or resid 14...A10 - 12
121(chain A and (resid 10 through 12 or resid 14...A14 - 33
131(chain A and (resid 10 through 12 or resid 14...A35 - 71
141(chain A and (resid 10 through 12 or resid 14...A10 - 124
151(chain A and (resid 10 through 12 or resid 14...A10 - 124
161(chain A and (resid 10 through 12 or resid 14...A116
171(chain A and (resid 10 through 12 or resid 14...A11116
181(chain A and (resid 10 through 12 or resid 14...A118 - 124
211(chain B and (resid 10 through 12 or resid 14...B10 - 12
221(chain B and (resid 10 through 12 or resid 14...B14 - 33
231(chain B and (resid 10 through 12 or resid 14...B35 - 71
241(chain B and (resid 10 through 12 or resid 14...B73
251(chain B and (resid 10 through 12 or resid 14...B75 - 97
261(chain B and (resid 10 through 12 or resid 14...B99 - 114
271(chain B and (resid 10 through 12 or resid 14...B116
281(chain B and (resid 10 through 12 or resid 14...B118 - 124

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12610.091 Da / Num. of mol.: 2 / Mutation: D38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P02766
#2: Chemical ChemComp-1FL / 5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Diflunisal


Mass: 250.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8F2O3 / Comment: antiinflammatory*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% (W/V) PEG-400, 0.1M Sodium Acetate, 0.2M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→64.15 Å / Num. obs: 38734 / % possible obs: 99.6 % / Redundancy: 12.754 % / Biso Wilson estimate: 25.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.041 / Χ2: 1.065 / Net I/σ(I): 33.03 / Num. measured all: 494029
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.5410.980.7522.9330194283527500.9090.78897
1.54-1.5813.1150.5064.9936065275227500.9660.52699.9
1.58-1.6313.2830.3557.0735479267326710.9880.36999.9
1.63-1.6813.1580.2699.2434565262726270.9920.279100
1.68-1.7313.0190.20511.7532937253025300.9940.214100
1.73-1.7912.4370.1516.0530409244524450.9950.157100
1.79-1.8612.2260.10322.129024237923740.9970.10899.8
1.86-1.9413.4730.07531.5130772228422840.9990.078100
1.94-2.0213.3490.05839.8929248219221910.9990.061100
2.02-2.1213.2060.0544.1427679209620960.9990.052100
2.12-2.2312.7820.04249.8525551200619990.9990.04499.7
2.23-2.3712.1880.0451.3623328192119140.9990.04199.6
2.37-2.5313.6230.03757.4724426179317930.9990.039100
2.53-2.7413.380.03761.0122358167116710.9990.038100
2.74-312.860.03663.4219868154515450.9990.037100
3-3.3511.640.03362.7316517143114190.9990.03599.2
3.35-3.87130.03469.2816120124512400.9990.03599.6
3.87-4.7412.8930.03370.7413860107710750.9990.03599.8
4.74-6.711.5150.03465.997658588480.9990.03698.8
6.7-64.1511.4530.03965.1258645125120.9990.041100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSJan 26, 2018data reduction
XSCALEJan 26, 2018data scaling
RefinementResolution: 1.499→64.15 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 3871 10 %
Rwork0.1884 34846 -
obs0.1908 38717 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.1 Å2 / Biso mean: 34.3845 Å2 / Biso min: 17.9 Å2
Refinement stepCycle: final / Resolution: 1.499→64.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 36 78 1892
Biso mean--62.02 35.77 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051923
X-RAY DIFFRACTIONf_angle_d0.8112641
X-RAY DIFFRACTIONf_chiral_restr0.081293
X-RAY DIFFRACTIONf_plane_restr0.006336
X-RAY DIFFRACTIONf_dihedral_angle_d21.242681
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A938X-RAY DIFFRACTION4.96TORSIONAL
12B938X-RAY DIFFRACTION4.96TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4993-1.51750.35181290.31621159128894
1.5175-1.53670.32071370.265612291366100
1.5367-1.5570.28221360.241112261362100
1.557-1.57830.26881370.237412311368100
1.5783-1.60090.23561370.21112481385100
1.6009-1.62470.24241320.200511821314100
1.6247-1.65010.23881400.210812521392100
1.6501-1.67720.24151340.19812221356100
1.6772-1.70610.26921370.218112351372100
1.7061-1.73710.25191380.229112391377100
1.7371-1.77060.26581350.22412191354100
1.7706-1.80670.25481400.224312621402100
1.8067-1.8460.18531340.195912041338100
1.846-1.88890.23831390.187912451384100
1.8889-1.93620.19131380.185712461384100
1.9362-1.98850.18781380.176812401378100
1.9885-2.0470.22791380.185912401378100
2.047-2.11310.2251360.189712301366100
2.1131-2.18860.20111410.193112641405100
2.1886-2.27630.21061370.18681239137699
2.2763-2.37990.22761390.18791244138399
2.3799-2.50540.19691400.18912621402100
2.5054-2.66230.21081390.205812531392100
2.6623-2.86790.2731410.195612681409100
2.8679-3.15650.20291400.204612661406100
3.1565-3.61320.19391430.1721278142199
3.6132-4.55210.16841430.156812951438100
4.5521-64.20880.22711530.18991368152199
Refinement TLS params.Method: refined / Origin x: 44.0379 Å / Origin y: 29.8737 Å / Origin z: 80.2377 Å
111213212223313233
T0.1875 Å20.0138 Å2-0.0017 Å2-0.1598 Å2-0.0078 Å2--0.1979 Å2
L0.5828 °2-0.0801 °2-0.1968 °2-0.961 °2-0.2587 °2--1.7373 °2
S-0.0127 Å °0.0406 Å °-0.139 Å °-0.1252 Å °-0.0587 Å °0.023 Å °0.1066 Å °-0.052 Å °0.0626 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 124
2X-RAY DIFFRACTION1allB10 - 124
3X-RAY DIFFRACTION1allC1 - 59
4X-RAY DIFFRACTION1allC60 - 78
5X-RAY DIFFRACTION1allD1 - 2

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