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- PDB-4tl5: Crystal Structure of Human Transthyretin Ser85Pro Mutant -

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Basic information

Entry
Database: PDB / ID: 4tl5
TitleCrystal Structure of Human Transthyretin Ser85Pro 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: 1.44 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 28, 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)27,9184
Polymers27,8592
Non-polymers582
Water1,874104
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8358
Polymers55,7184
Non-polymers1174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6830 Å2
ΔGint-94 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.170, 85.800, 63.870
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-304-

HOH

21B-307-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13929.608 Da / Num. of mol.: 2 / Fragment: UNP residues 29-147 / Mutation: S85P
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
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: 1.44→51.233 Å / Num. obs: 43105 / % possible obs: 98.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.96 Å2 / Net I/σ(I): 14.78
Reflection shellMean I/σ(I) obs: 1.45 / % possible all: 88.3

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Processing

Software
NameVersionClassificationNB
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
XSCALEdata scaling
RefinementResolution: 1.44→51.23 Å / Cor.coef. Fo:Fc: 0.9465 / Cor.coef. Fo:Fc free: 0.9465 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 2165 5.03 %RANDOM
Rwork0.1924 ---
obs0.1927 43068 98.45 %-
Displacement parametersBiso max: 92.15 Å2 / Biso mean: 24.41 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.9915 Å20 Å20 Å2
2--3.8796 Å20 Å2
3----0.8881 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: final / Resolution: 1.44→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 2 104 1891
Biso mean--36.44 30.06 -
Num. residues----231
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d603SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes273HARMONIC5
X-RAY DIFFRACTIONt_it1845HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion249SEMIHARMONIC5
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_contact2111SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1845HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2524HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.17
X-RAY DIFFRACTIONt_other_torsion16.15
LS refinement shellResolution: 1.44→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2401 135 4.97 %
Rwork0.219 2584 -
all0.22 2719 -
obs--98.45 %
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)
10.32870.1533-0.26871.3277-0.30880.6408-0.0340.06420.0914-0.1314-0.01040.05070.02320.03060.0444-0.0168-0.00620.0005-0.01520.019-0.026519.337312.8092-25.6774
20.5269-0.2907-0.0810.6704-0.00820.5814-0.029-0.04260.09070.0844-0.0227-0.02770.0334-0.01180.0517-0.01150.00680.002-0.02-0.0173-0.012521.948713.2963-6.165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 125
2X-RAY DIFFRACTION2{ B|* }B10 - 124

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