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- PDB-6e77: Structure of Human Transthyretin Asp38Ala Mutant in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+77
TitleStructure of Human Transthyretin Asp38Ala 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: 1.6 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)25,7404
Polymers25,1242
Non-polymers6162
Water1,63991
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4818
Polymers50,2484
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)42.460, 85.070, 64.510
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

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12562.093 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-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.: 91 / 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: 46.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M Ammonium sulfate, 0.1M Sodium citrate, 0.2M Potassium sodium tartrate tetrahydrate

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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→19.62 Å / Num. obs: 31384 / % possible obs: 99.3 % / Redundancy: 5.426 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.069 / Χ2: 1.049 / Net I/σ(I): 14.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.645.5390.4883.3323000.9380.53898.4
1.64-1.695.6510.4083.9921950.9420.44999.2
1.69-1.745.5310.3244.921430.9670.35799.4
1.74-1.795.5060.2785.7921340.9690.30799.3
1.79-1.855.2740.217.2920460.9770.23299.2
1.85-1.915.1360.159.6219740.9870.16799.6
1.91-1.985.6930.12612.1219150.9910.13899.6
1.98-2.075.6610.10614.1418380.9930.11799.6
2.07-2.165.5780.09215.7917950.9950.10299.6
2.16-2.265.4620.0817.716930.9940.08899.6
2.26-2.395.0270.07417.6116260.9940.08299.6
2.39-2.535.4820.07119.4515300.9950.07899.7
2.53-2.75.620.06621.4414520.9950.07399.7
2.7-2.925.4950.0623.4413670.9970.06699.6
2.92-3.25.3270.05424.9712550.9970.0699.7
3.2-3.584.7980.04825.4511510.9970.05499.1
3.58-4.135.5280.04728.9810120.9980.05399.7
4.13-5.065.3040.04629.538780.9960.05199.7
5.06-7.164.8180.04627.176940.9980.05298.6
7.16-19.625.2360.04328.63860.9980.04993.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.6→19.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.085 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3139 10 %RANDOM
Rwork0.183 ---
obs0.185 31383 99.4 %-
Displacement parametersBiso max: 102.86 Å2 / Biso mean: 27.85 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--5.2069 Å20 Å20 Å2
2--4.4937 Å20 Å2
3---0.7132 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.6→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 40 91 1903
Biso mean--20.78 33.93 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d616SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes285HARMONIC5
X-RAY DIFFRACTIONt_it1898HARMONIC20
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_contact2122SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1898HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2600HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion16.37
LS refinement shellResolution: 1.6→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2073 281 10 %
Rwork0.1874 2529 -
all0.1896 2810 -
obs--98.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72310.17150.00551.44530.52630.7904-0.05170.0949-0.1372-0.1361-0.0241-0.02150.0226-0.080.0757-0.0198-0.00370.0007-0.0301-0.0234-0.031644.770829.782170.7607
20.9749-0.3548-0.06920.9947-0.19480.6595-0.0587-0.0398-0.12980.0778-0.01640.0050.00520.01180.0751-0.01580.0052-0.0022-0.0390.0162-0.013942.208729.341590.485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 124
2X-RAY DIFFRACTION2{ B|* }B10 - 124

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