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- PDB-6e74: Structure of Human Transthyretin Leu55Pro Mutant in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+74
TitleStructure of Human Transthyretin Leu55Pro Mutant in Complex with Tafamidis
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / tafamidis
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, 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: 1.6 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)25,7964
Polymers25,1802
Non-polymers6162
Water97354
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5938
Polymers50,3604
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)42.890, 84.620, 65.130
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

31B-201-

3MI

41B-201-

3MI

51B-201-

3MI

61B-324-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12590.060 Da / Num. of mol.: 2 / Mutation: L55P
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.: 54 / 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: 47.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, 30% PEG monomethyl ether 550

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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: 1.6→19.8 Å / Num. obs: 31902 / % possible obs: 99.6 % / Redundancy: 5.71 % / Biso Wilson estimate: 25.56 Å2 / Net I/σ(I): 16.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.645.7581.2421.7323000.5371.36599.1
1.64-1.695.9111.0712.1122460.6191.17599.5
1.69-1.745.7770.862.6722090.7360.94699.7
1.74-1.795.6560.6683.5421520.8430.73699.8
1.79-1.855.5310.4545.2120760.9230.50199.7
1.85-1.915.360.37.6120110.9630.33399.7
1.91-1.986.0420.22510.2719530.9820.24699.9
1.98-2.075.9680.16412.5418910.990.179100
2.07-2.165.9450.13214.8418140.9910.14499.9
2.16-2.265.770.10118.1617290.9940.11199.8
2.26-2.395.390.08819.2516480.9950.09899.9
2.39-2.535.8350.07322.0415650.9970.0899.9
2.53-2.76.0390.06326.214790.9970.06999.9
2.7-2.925.9080.05230.3213750.9970.05899.8
2.92-3.25.6020.04434.5612750.9980.04899.8
3.2-3.585.0290.03637.9811580.9980.0498.9
3.58-4.135.7840.03344.6410370.9990.03699.6
4.13-5.065.6230.02947.438800.9990.03299.2
5.06-7.164.9480.02842.227130.9990.03299.6
7.16-19.85.3790.02445.7439110.02793.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.6→19.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.085 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3190 10 %RANDOM
Rwork0.19 ---
obs0.192 31900 99.7 %-
Displacement parametersBiso max: 114.42 Å2 / Biso mean: 31.49 Å2 / Biso min: 14.31 Å2
Baniso -1Baniso -2Baniso -3
1--5.2455 Å20 Å20 Å2
2--4.7538 Å20 Å2
3---0.4917 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 40 54 1870
Biso mean--27.77 33.88 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d620SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1916HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion252SEMIHARMONIC5
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_contact2084SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1916HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2628HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.01
X-RAY DIFFRACTIONt_other_torsion15.94
LS refinement shellResolution: 1.6→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3125 287 9.99 %
Rwork0.2906 2585 -
all0.2927 2872 -
obs--99.1 %
Refinement TLS params.Method: refined / Origin x: 43.7015 Å / Origin y: 29.6404 Å / Origin z: 81.2148 Å
111213212223313233
T-0.1012 Å20.0005 Å2-0.0088 Å2-0.0087 Å2-0.0101 Å2---0.0537 Å2
L0.501 °2-0.0368 °2-0.2949 °2-1.4831 °20.0246 °2--0.7642 °2
S-0.0727 Å °0.0399 Å °-0.17 Å °0.0336 Å °-0.0027 Å °-0.0138 Å °0.0458 Å °-0.0253 Å °0.0755 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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