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- PDB-5tzl: Structure of transthyretin in complex with the kinetic stabilizer 201 -

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Basic information

Entry
Database: PDB / ID: 5tzl
TitleStructure of transthyretin in complex with the kinetic stabilizer 201
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / kinetic stabilizer
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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
4-(7-chloro-1,3-benzoxazol-2-yl)-2,6-diiodophenol / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsConnelly, S. / Mortenson, D.E. / Choi, S. / Wilson, I.A. / Powers, E.T. / Kelly, J.W. / Johnson, S.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK 46335 United States
The Skaggs Institute of Chemical Biology United States
Lita Annenberg Hazen Foundation United States
Indiana University School of Medicine, Department of Biochemistry and Molecular Biology United States
The George E. Hewitt Foundation for Medical Research United States
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Semi-quantitative models for identifying potent and selective transthyretin amyloidogenesis inhibitors.
Authors: Connelly, S. / Mortenson, D.E. / Choi, S. / Wilson, I.A. / Powers, E.T. / Kelly, J.W. / Johnson, S.M.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)28,6464
Polymers27,6512
Non-polymers9952
Water4,360242
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2918
Polymers55,3014
Non-polymers1,9904
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6293 Å2
ΔGint-39.9 kcal/mol
Surface area19294 Å2
Unit cell
Length a, b, c (Å)43.265, 85.467, 64.285
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-

IIH

21A-201-

IIH

31A-201-

IIH

41A-201-

IIH

51B-201-

IIH

61B-201-

IIH

71A-414-

HOH

81A-438-

HOH

91A-448-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13825.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-IIH / 4-(7-chloro-1,3-benzoxazol-2-yl)-2,6-diiodophenol / 2-(3,5-Diiodo-4-hydroxyphenyl)-7-chlorobenzoxazole


Mass: 497.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H6ClI2NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: WT-TTR at 4 mg/mL and five-fold molar excess compound 201 crystallized from solution containing 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. Crystals cryoprotected by addition of 10% (v/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.99184 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 47590 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.041 / Net I/σ(I): 28.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FBR

2fbr


Resolution: 1.4→33.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.004 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16721 2409 5.1 %RANDOM
Rwork0.13256 ---
obs0.13429 45137 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0 Å2
2--1.07 Å20 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 1.4→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 38 242 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191927
X-RAY DIFFRACTIONr_bond_other_d0.0020.021744
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9152653
X-RAY DIFFRACTIONr_angle_other_deg0.8712.9874040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09523.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67915287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.858158
X-RAY DIFFRACTIONr_chiral_restr0.1160.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0192366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr9.33633671
X-RAY DIFFRACTIONr_sphericity_free46.155586
X-RAY DIFFRACTIONr_sphericity_bonded22.11253767
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 183 -
Rwork0.236 3249 -
obs--99.19 %

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