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- PDB-5cr1: Crystal structure of TTR/resveratrol/T4 complex -

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Basic information

Entry
Database: PDB / ID: 5cr1
TitleCrystal structure of TTR/resveratrol/T4 complex
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloid / fibrillogenesis / fibrillogenesis inhibitors / polyphenols / polyphenol metabolites / transthyretin / negative cooperativity
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
RESVERATROL / 3,5,3',5'-TETRAIODO-L-THYRONINE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.545 Å
AuthorsZanotti, G. / Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Berni, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Transthyretin Binding Heterogeneity and Anti-amyloidogenic Activity of Natural Polyphenols and Their Metabolites.
Authors: Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_symm_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_symm_contact.auth_atom_id_2
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3594
Polymers25,3542
Non-polymers1,0052
Water2,900161
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7198
Polymers50,7094
Non-polymers2,0104
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9030 Å2
ΔGint-29 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.536, 85.633, 63.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

T44

21B-201-

STL

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12677.137 Da / Num. of mol.: 2 / Fragment: UNP residues 30-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pGEM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The protein (5 mg/ml), in 20 mM sodium phosphate, pH 7 was incubated with a reservoir solution containing 2.2 M ammonium sulphate, 0.1 M KCl, 0.03 M sodium phosphate, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→42.82 Å / Num. obs: 43821 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 21.3
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.545→42.816 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3253 5 %Random selection
Rwork0.1664 ---
obs0.1677 34821 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.545→42.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 41 161 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011843
X-RAY DIFFRACTIONf_angle_d1.2872519
X-RAY DIFFRACTIONf_dihedral_angle_d13.537649
X-RAY DIFFRACTIONf_chiral_restr0.052286
X-RAY DIFFRACTIONf_plane_restr0.01322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5449-1.5680.21721310.21082454X-RAY DIFFRACTION89
1.568-1.59250.2571420.22675X-RAY DIFFRACTION100
1.5925-1.61860.20531470.19042747X-RAY DIFFRACTION100
1.6186-1.64650.24721430.18562695X-RAY DIFFRACTION100
1.6465-1.67650.19431410.18542728X-RAY DIFFRACTION100
1.6765-1.70870.22361430.17792713X-RAY DIFFRACTION100
1.7087-1.74360.18271440.17442717X-RAY DIFFRACTION99
1.7436-1.78150.21281430.18392686X-RAY DIFFRACTION99
1.7815-1.82290.21881420.1822717X-RAY DIFFRACTION99
1.8229-1.86850.19361400.17832731X-RAY DIFFRACTION100
1.8685-1.91910.23041440.18392680X-RAY DIFFRACTION98
1.9191-1.97550.21721430.16612704X-RAY DIFFRACTION100
1.9755-2.03930.1771420.15532721X-RAY DIFFRACTION100
2.0393-2.11220.20581410.15562697X-RAY DIFFRACTION100
2.1122-2.19670.17261400.15372755X-RAY DIFFRACTION100
2.1967-2.29670.21561340.17132562X-RAY DIFFRACTION95
2.2967-2.41780.1841430.16762707X-RAY DIFFRACTION99
2.4178-2.56930.19431420.1712733X-RAY DIFFRACTION100
2.5693-2.76760.20961440.16522708X-RAY DIFFRACTION99
2.7676-3.0460.17831460.17572728X-RAY DIFFRACTION99
3.046-3.48660.17831390.1662614X-RAY DIFFRACTION96
3.4866-4.39210.19631370.14322664X-RAY DIFFRACTION98
4.3921-42.83290.1691420.16152702X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.9915 Å / Origin y: 29.8884 Å / Origin z: 47.6584 Å
111213212223313233
T0.1043 Å20.0039 Å2-0.0081 Å2-0.1067 Å20.0002 Å2--0.1195 Å2
L0.475 °20.0745 °2-0.1186 °2-0.7835 °20.0561 °2--0.5639 °2
S-0.0333 Å °-0.0144 Å °-0.1106 Å °0.0361 Å °-0.0109 Å °0.0006 Å °0.0259 Å °0.0134 Å °-0.0011 Å °
Refinement TLS groupSelection details: all

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