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- PDB-4tls: Crystal Structure of Human Transthyretin Glu92Pro Mutant -

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Basic information

Entry
Database: PDB / ID: 4tls
TitleCrystal Structure of Human Transthyretin Glu92Pro Mutant
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / mutant
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/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
PHOSPHATE ION / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 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 30, 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 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)28,0806
Polymers27,7752
Non-polymers3054
Water2,000111
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,16012
Polymers55,5504
Non-polymers6108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8220 Å2
ΔGint-107 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.380, 86.080, 64.360
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-303-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13887.572 Da / Num. of mol.: 2 / Fragment: UNP residues 29-147 / Mutation: E92P
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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: 1.35→64.36 Å / Num. obs: 52487 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 17.19 Å2 / Net I/σ(I): 14.15

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Processing

Software
NameVersionClassificationNB
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
XSCALEdata scaling
RefinementResolution: 1.35→64.36 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9598 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.05 / SU Rfree Cruickshank DPI: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 2675 5.1 %RANDOM
Rwork0.1854 ---
obs0.1857 52487 99.9 %-
Displacement parametersBiso max: 91.61 Å2 / Biso mean: 22.1 Å2 / Biso min: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.8304 Å20 Å20 Å2
2--2.9003 Å20 Å2
3----1.0699 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: final / Resolution: 1.35→64.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 23 111 1908
Biso mean--24.98 29.33 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d595SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes268HARMONIC5
X-RAY DIFFRACTIONt_it1843HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion245SEMIHARMONIC5
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_contact2088SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1843HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2516HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion4.5
X-RAY DIFFRACTIONt_other_torsion15.85
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2389 195 5.12 %
Rwork0.2249 3615 -
all0.2256 3810 -
obs--99.9 %
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)
10.50410.21320.23971.2820.42860.5679-0.04740.0946-0.03-0.0572-0.0125-0.0777-0.02030.01250.06-0.0214-0.0043-0.0125-0.0192-0.0103-0.013744.689830.209270.6787
20.6649-0.38680.09570.8862-0.21320.6327-0.0169-0.0751-0.0750.1204-0.0310.05720.00050.0070.0479-0.00530.0013-0.016-0.03260.0071-0.013942.000629.717390.4142
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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