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- PDB-5jiq: Crystal Structure of Human Transthyretin in Complex with 2,2',4,4... -

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Basic information

Entry
Database: PDB / ID: 5jiq
TitleCrystal Structure of Human Transthyretin in Complex with 2,2',4,4'-tetrahydroxybenzophenone (BP2)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine binding / 2 / 2' / 4 / 4'-tetrahydroxybenzophenone (BP2)
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase 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/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
bis(2,4-dihydroxyphenyl)methanone / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBegum, A. / Zhang, J. / Olofsson, A. / Andersson, P. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Environ. Sci. Technol. / Year: 2016
Title: Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.
Authors: Zhang, J. / Begum, A. / Brannstrom, K. / Grundstrom, C. / Iakovleva, I. / Olofsson, A. / Sauer-Eriksson, A.E. / Andersson, P.L.
#1: Journal: Plos One / Year: 2016
Title: Tetrabromobisphenol A Is an Efficient Stabilizer of the Transthyretin Tetramer.
Authors: Iakovleva, I. / Begum, A. / Brannstrom, K. / Wijsekera, A. / Nilsson, L. / Zhang, J. / Andersson, P.L. / Sauer-Eriksson, A.E. / Olofsson, A.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)28,1626
Polymers27,5552
Non-polymers6084
Water4,324240
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32412
Polymers55,1094
Non-polymers1,2158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.943, 85.497, 64.191
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-

27M

21B-201-

27M

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 13777.360 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-27M / bis(2,4-dihydroxyphenyl)methanone


Mass: 246.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. BP2 was added at 5 x molar excess to the protein. The reservoir ...Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. BP2 was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent glycerol at pH 5.5. Drop size 3 plus 3 microliter.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.913 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. obs: 42623 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 23.35
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.74 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f41

1f41


Resolution: 1.45→38.374 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.93
RfactorNum. reflection% reflection
Rfree0.1677 2147 5.04 %
Rwork0.1314 --
obs0.1332 42619 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→38.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 43 240 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092107
X-RAY DIFFRACTIONf_angle_d1.2212908
X-RAY DIFFRACTIONf_dihedral_angle_d14.723758
X-RAY DIFFRACTIONf_chiral_restr0.074312
X-RAY DIFFRACTIONf_plane_restr0.008390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4481-1.48180.29111390.20852486X-RAY DIFFRACTION92
1.4818-1.51880.2271220.16922682X-RAY DIFFRACTION100
1.5188-1.55990.22951470.14372650X-RAY DIFFRACTION100
1.5599-1.60580.16741520.12322674X-RAY DIFFRACTION100
1.6058-1.65760.15031460.11472665X-RAY DIFFRACTION100
1.6576-1.71680.17911510.11422700X-RAY DIFFRACTION100
1.7168-1.78560.1761520.11512671X-RAY DIFFRACTION100
1.7856-1.86690.17441490.11232666X-RAY DIFFRACTION100
1.8669-1.96530.13151430.10592691X-RAY DIFFRACTION100
1.9653-2.08840.14781380.1122725X-RAY DIFFRACTION100
2.0884-2.24960.13911370.11132704X-RAY DIFFRACTION100
2.2496-2.4760.18361430.12672722X-RAY DIFFRACTION100
2.476-2.83420.17891480.13632740X-RAY DIFFRACTION100
2.8342-3.57030.16411490.13682782X-RAY DIFFRACTION100
3.5703-38.38790.1671310.14482914X-RAY DIFFRACTION100

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