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- PDB-6e71: Structure of Human Transthyretin Val30Met/Thr119Met Mutant -

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Basic information

Entry
Database: PDB / ID: 6.0E+71
TitleStructure of Human Transthyretin Val30Met/Thr119Met Mutant
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin
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, 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
DI(HYDROXYETHYL)ETHER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsSaelices, L. / Chung, K. / 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)25,4433
Polymers25,3372
Non-polymers1061
Water1,910106
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8856
Polymers50,6734
Non-polymers2122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area7130 Å2
ΔGint-44 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.140, 86.540, 63.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12668.260 Da / Num. of mol.: 2 / Mutation: V30M,T119M
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium Sulfate, 0.1M Tris, 30% (w/v) PEG 4000

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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: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→43.27 Å / Num. obs: 38230 / % possible obs: 98 % / Redundancy: 3.249 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.056 / Χ2: 0.983 / Net I/σ(I): 13.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.2140.9071.5428200.5111.08398.7
1.54-1.583.2480.7011.9927140.6630.83798.8
1.58-1.633.2640.5872.5726410.7170.69997.9
1.63-1.683.1120.4873.0125810.80.58497.5
1.68-1.733.1290.3973.7424760.8570.47497.4
1.73-1.793.3480.2955.2624370.9190.34999.4
1.79-1.863.3540.2137.1623430.9570.25199
1.86-1.943.3370.1419.8622750.9810.16698.6
1.94-2.023.0730.10411.9721440.9870.12497.7
2.02-2.123.3420.08414.5320780.9920.198.3
2.12-2.243.4150.06418.4619790.9950.07598.8
2.24-2.373.3530.05819.4118850.9950.06998.5
2.37-2.543.2140.04921.6517750.9960.05898.6
2.54-2.743.2070.03824.6916180.9980.04696.6
2.74-33.3940.03430.0715370.9980.0498.4
3-3.363.2950.02734.1113850.9990.03296.8
3.36-3.883.0310.02338.9111650.9990.02893.3
3.88-4.753.2910.02144.310580.9990.02598
4.75-6.713.1320.0242.48310.9990.02596.9
6.71-43.272.9060.0239.984880.9990.02594.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.5→43.27 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3823 10 %RANDOM
Rwork0.191 ---
obs0.193 38229 98 %-
Displacement parametersBiso max: 169.71 Å2 / Biso mean: 24.46 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.1531 Å20 Å20 Å2
2--1.0177 Å20 Å2
3---0.1354 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.5→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 7 106 1895
Biso mean--43.25 33.17 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d635SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes321HARMONIC5
X-RAY DIFFRACTIONt_it1879HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion251SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2169SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1879HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2563HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion15.04
LS refinement shellResolution: 1.5→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.351 76 9.93 %
Rwork0.2931 689 -
all0.2992 765 -
obs--98.03 %
Refinement TLS params.Method: refined / Origin x: 44.0529 Å / Origin y: 30.1465 Å / Origin z: 79.9095 Å
111213212223313233
T-0.059 Å20.003 Å2-0.0049 Å2--0.0051 Å2-0.0025 Å2---0.0172 Å2
L0.2258 °2-0.0514 °2-0.1004 °2-0.8597 °2-0.032 °2--0.4334 °2
S-0.0332 Å °-0.0012 Å °-0.0828 Å °-0.0458 Å °-0.0163 Å °-0.0178 Å °0.0187 Å °-0.0167 Å °0.0495 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A10 - 124
2X-RAY DIFFRACTION1{ *|* }B10 - 124
3X-RAY DIFFRACTION1{ *|* }C10 - 124
4X-RAY DIFFRACTION1{ *|* }D10 - 124

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