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- PDB-6e73: Structure of Human Transthyretin Val30Met Mutant in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+73
TitleStructure of Human Transthyretin Val30Met Mutant in Complex with Diflunisal
ComponentsTransthyretin
KeywordsPROTEIN BINDING / 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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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 / ACETATE ION / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.797 Å
AuthorsChung, K. / Saelices, L. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.S.
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. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
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 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8365
Polymers25,2762
Non-polymers5593
Water81145
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,67210
Polymers50,5534
Non-polymers1,1196
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8960 Å2
ΔGint-48 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.080, 84.800, 64.240
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

21A-201-

1FL

31B-201-

1FL

41B-201-

1FL

51B-201-

1FL

61B-201-

1FL

71B-201-

1FL

81B-201-

1FL

91B-313-

HOH

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:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSLEULEU(chain A and (resid 10 through 12 or resid 14...AA10 - 121 - 3
12VALVALPHEPHE(chain A and (resid 10 through 12 or resid 14...AA14 - 335 - 24
13LYSLYSVALVAL(chain A and (resid 10 through 12 or resid 14...AA35 - 7126 - 62
14ILEILETYRTYR(chain A and (resid 10 through 12 or resid 14...AA73 - 11464 - 105
15TYRTYRASNASN(chain A and (resid 10 through 12 or resid 14...AA116 - 124107 - 115
21CYSCYSLEULEU(chain B and (resid 10 through 12 or resid 14...BB10 - 121 - 3
22VALVALPHEPHE(chain B and (resid 10 through 12 or resid 14...BB14 - 335 - 24
23LYSLYSVALVAL(chain B and (resid 10 through 12 or resid 14...BB35 - 7126 - 62
24ILEILETYRTYR(chain B and (resid 10 through 12 or resid 14...BB73 - 11464 - 105
25TYRTYRASNASN(chain B and (resid 10 through 12 or resid 14...BB116 - 124107 - 115

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12638.168 Da / Num. of mol.: 2 / Mutation: V30M
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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (W/V) PEG-1000, 0.1M Imidazole, 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 23, 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: 1.8→64.24 Å / Num. obs: 22422 / % possible obs: 99.2 % / Redundancy: 6.443 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.045 / Χ2: 1.105 / Net I/σ(I): 21.24 / Num. measured all: 144471
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.845.760.4942.9315220.9540.54293.8
1.84-1.896.8010.3384.8215950.9830.36599.7
1.89-1.956.7880.2546.6815690.9850.27599.8
1.95-2.016.7170.1948.7115030.9870.21199.8
2.01-2.086.640.14910.8814650.9940.16299.7
2.08-2.156.5810.11913.4814360.9950.12999.7
2.15-2.236.3770.08817.0413510.9960.09699.8
2.23-2.325.8460.07917.8313220.9960.08799.5
2.32-2.426.7390.07220.4412840.9970.07899.9
2.42-2.546.8770.06124.6312180.9980.06699.8
2.54-2.686.7270.05327.7611660.9980.05899.7
2.68-2.846.6070.0530.8710850.9980.05499.5
2.84-3.046.4580.04534.2310520.9970.04999.7
3.04-3.285.8760.0435.349750.9980.04499.5
3.28-3.596.1770.03540.538950.9990.03998.9
3.59-4.026.5520.03643.548170.9980.03999.5
4.02-4.646.4260.03245.047320.9990.03599.7
4.64-5.686.1190.03344.356290.9990.03699.8
5.68-8.045.5470.03440.495050.9980.03799
8.04-64.245.9470.03142.643010.9990.03499.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.797→64.24 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 2240 10 %
Rwork0.1868 20153 -
obs0.1902 22393 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.93 Å2 / Biso mean: 45.2874 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.797→64.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 40 45 1865
Biso mean--77.33 46.57 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061915
X-RAY DIFFRACTIONf_angle_d0.8462617
X-RAY DIFFRACTIONf_chiral_restr0.061288
X-RAY DIFFRACTIONf_plane_restr0.006335
X-RAY DIFFRACTIONf_dihedral_angle_d15.631120
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1002X-RAY DIFFRACTION6.325TORSIONAL
12B1002X-RAY DIFFRACTION6.325TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.797-1.83610.33311270.2971132125992
1.8361-1.87880.25081410.23631265140699
1.8788-1.92580.24061350.212412171352100
1.9258-1.97780.2351390.197712551394100
1.9778-2.0360.2381380.196612381376100
2.036-2.10180.26221380.187312441382100
2.1018-2.17690.22841400.187412561396100
2.1769-2.2640.21721400.176412651405100
2.264-2.36710.27311390.199512491388100
2.3671-2.49190.21321410.196812661407100
2.4919-2.6480.25461390.183312521391100
2.648-2.85250.22061420.197112801422100
2.8525-3.13950.24931410.204312701411100
3.1395-3.59380.21311430.16971285142899
3.5938-4.52760.17271450.159113011446100
4.5276-64.28110.2231520.19711378153099
Refinement TLS params.Method: refined / Origin x: 43.9851 Å / Origin y: 29.6449 Å / Origin z: 80.249 Å
111213212223313233
T0.2758 Å20.0017 Å2-0.0136 Å2-0.2049 Å2-0.0171 Å2--0.2726 Å2
L1.2909 °2-0.0424 °2-0.5858 °2-1.1495 °2-0.1614 °2--1.6029 °2
S-0.026 Å °0.0746 Å °-0.2148 Å °-0.0159 Å °-0.0184 Å °0.0071 Å °0.1058 Å °-0.0335 Å °0.0359 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 124
2X-RAY DIFFRACTION1allB10 - 124
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 36
5X-RAY DIFFRACTION1allD37 - 45
6X-RAY DIFFRACTION1allF1

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