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- PDB-4tkw: Crystal Structure of Human Transthyretin Leu55Pro Mutant -

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Basic information

Entry
Database: PDB / ID: 4tkw
TitleCrystal Structure of Human Transthyretin Leu55Pro Mutant
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / mutant
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/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSaelices, L. / Cascio, D. / Sawaya, M. / Eisenberg, D.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Uncovering the Mechanism of Aggregation of Human Transthyretin.
Authors: Saelices, L. / Johnson, L.M. / Liang, W.Y. / Sawaya, M.R. / Cascio, D. / Ruchala, P. / Whitelegge, J. / Jiang, L. / Riek, R. / Eisenberg, D.S.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Dec 27, 2023Group: 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


Theoretical massNumber of molelcules
Total (without water)27,8072
Polymers27,8072
Non-polymers00
Water99155
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,6144
Polymers55,6144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area6270 Å2
ΔGint-44 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.060, 84.400, 65.090
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: 13903.528 Da / Num. of mol.: 2 / Fragment: UNP residues 29-147 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion / 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: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
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→19.87 Å / Num. obs: 22582 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.26 % / Biso Wilson estimate: 28.82 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.098 / Χ2: 1.016 / Net I/σ(I): 10.84 / Num. measured all: 142122
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.855.690.6811.1211.589256162815981.23398.2
1.85-1.90.8130.8852.2710724160416010.95899.8
1.9-1.950.8770.6383.0310506158015780.69299.9
1.95-2.010.9170.513.8110024152315190.55499.7
2.01-2.080.9510.4044.569437145714540.43999.8
2.08-2.150.9660.3285.468945144214390.35899.8
2.15-2.230.9670.2516.758121137713700.27599.5
2.23-2.320.9850.2287.859001134113390.24899.9
2.32-2.430.9830.2038.768458127412720.22199.8
2.43-2.550.9860.16610.398118124112390.18199.8
2.55-2.680.9910.13612.017295116111570.14899.7
2.68-2.850.9920.1113.866240110510990.12199.5
2.85-3.040.9940.08917.996911106010560.09799.6
3.04-3.290.9950.07420.8163659899850.0899.6
3.29-3.60.9970.06324.3655889018990.06999.8
3.6-4.020.9970.05824.8946708258180.06499.2
4.02-4.650.9970.05126.9241937377330.05699.5
4.65-5.690.9980.04928.7938676346310.05499.5
5.69-8.050.9980.04725.9528255155110.05199.2
8.050.9990.03827.315783132840.04290.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
XSCALEdata scaling
RefinementResolution: 1.8→19.87 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9498 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.101
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1147 5.1 %RANDOM
Rwork0.1948 ---
obs0.195 22488 99.31 %-
Displacement parametersBiso max: 107.47 Å2 / Biso mean: 37.42 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--7.8593 Å20 Å20 Å2
2--7.0259 Å20 Å2
3---0.8334 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: final / Resolution: 1.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 55 1780
Biso mean---37.01 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d555SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes266HARMONIC5
X-RAY DIFFRACTIONt_it1773HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
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_contact1885SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1773HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2427HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion14.44
LS refinement shellResolution: 1.8→1.89 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2146 139 4.87 %
Rwork0.2091 2718 -
all0.2094 2857 -
obs--99.31 %
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)
11.91240.46-0.15073.8790.61011.1678-0.12180.2405-0.2155-0.30540.0444-0.12860.0669-0.10920.0775-0.0479-0.00720.0069-0.0694-0.0551-0.067145.677529.668671.6278
21.5207-0.70480.4082.1085-0.17330.7194-0.06370.0358-0.0410.2796-0.01870.1224-0.00810.02380.08240.01060.0130.0003-0.06440.009-0.039342.44229.157691.0593
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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