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- PDB-6e72: Structure of Human Transthyretin Val30Met Mutant in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+72
TitleStructure of Human Transthyretin Val30Met Mutant in Complex with Tafamidis
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / tafamidis
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
Chem-3MI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 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

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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)25,9894
Polymers25,3722
Non-polymers6162
Water1,838102
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9778
Polymers50,7454
Non-polymers1,2324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)43.040, 85.240, 63.890
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-

3MI

21A-201-

3MI

31A-201-

3MI

41B-201-

3MI

51B-201-

3MI

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12686.165 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-3MI / 2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid / Tafamidis


Mass: 308.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7Cl2NO3 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Lithium Sulfate Monohydrate, 20% (w/v) PEG 3350

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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: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→19.83 Å / Num. obs: 42335 / % possible obs: 99.7 % / Redundancy: 5.039 % / Biso Wilson estimate: 23.62 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.071 / Χ2: 1.06 / Net I/σ(I): 11.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.495.1090.7811.8731240.6910.873100
1.49-1.535.20.6212.4629800.8040.692100
1.53-1.575.160.4773.1829440.8850.531100
1.57-1.625.0890.3784.0328340.9260.42299.9
1.62-1.674.9040.3094.8427900.9360.34699.8
1.67-1.734.7810.245.926770.960.2799.8
1.73-1.85.2980.1987.8525800.9720.2299.7
1.8-1.875.210.1510.0525070.9830.16799.8
1.87-1.965.1390.11512.9223820.9890.12899.7
1.96-2.054.9970.09814.9122880.990.10999.8
2.05-2.164.6110.08116.3521730.990.09299.6
2.16-2.295.2050.07419.4120750.9920.08399.8
2.29-2.455.2210.07419.8519510.9930.08299.8
2.45-2.655.1380.06721.3918230.9950.07499.8
2.65-2.94.9370.06122.4116910.9940.06899.5
2.9-3.244.6240.05623.0315210.9960.06398.7
3.24-3.745.1450.05425.6413630.9970.0699.8
3.74-4.595.0130.0525.9611740.9960.05699.6
4.59-6.484.4680.04524.249280.9970.05199.1
6.48-19.834.8420.0525.025300.9960.05695.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.45→19.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4234 10 %RANDOM
Rwork0.187 ---
obs0.189 42334 99.8 %-
Displacement parametersBiso max: 103.23 Å2 / Biso mean: 28.47 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.2033 Å20 Å20 Å2
2--1.4988 Å20 Å2
3----1.2955 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: final / Resolution: 1.45→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 40 102 1928
Biso mean--23.24 35.22 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d638SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes334HARMONIC5
X-RAY DIFFRACTIONt_it1934HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion253SEMIHARMONIC5
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_contact2210SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1934HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2656HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.12
X-RAY DIFFRACTIONt_other_torsion15.75
LS refinement shellResolution: 1.45→1.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2151 85 10.04 %
Rwork0.2193 762 -
all0.2189 847 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 43.9926 Å / Origin y: 29.7986 Å / Origin z: 79.9059 Å
111213212223313233
T-0.0401 Å20.0051 Å2-0.0079 Å2--0.0441 Å2-0.0057 Å2---0.012 Å2
L0.4741 °2-0.0708 °2-0.1976 °2-0.8366 °20.0002 °2--0.5138 °2
S-0.0389 Å °0.0328 Å °-0.1133 Å °0.0029 Å °-0.0256 Å °-0.0059 Å °0.0066 Å °-0.0271 Å °0.0645 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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