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- PDB-6grp: Crystal Structure Of Human Transthyretin in complex with 3,5,6-tr... -

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Basic information

Entry
Database: PDB / ID: 6grp
TitleCrystal Structure Of Human Transthyretin in complex with 3,5,6-trichloro-2-pyridinol (TC2P)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / 3 / 5 / 6-trichloro-2-pyridinol / TC2P
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
3,5,6-trichloro-2-pyridinol / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGrundstrom, C. / Zhang, J. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Environ. Sci. Technol. / Year: 2018
Title: Interspecies Variation between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals.
Authors: Zhang, J. / Grundstrom, C. / Brannstrom, K. / Iakovleva, I. / Lindberg, M. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E.
#1: 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.
History
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Apr 24, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 17, 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 / 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)28,3717
Polymers27,5552
Non-polymers8175
Water5,026279
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,74314
Polymers55,1094
Non-polymers1,63310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)85.430, 42.820, 64.771
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-202-

F4Z

21A-202-

F4Z

31B-201-

F4Z

41B-201-

F4Z

51B-201-

F4Z

61B-404-

HOH

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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-F4Z / 3,5,6-trichloro-2-pyridinol


Mass: 198.434 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H2Cl3NO
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 42.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. TC2P was added at 5 x molar excess to the protein. The 1.65 M ...Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. TC2P was added at 5 x molar excess to the protein. The 1.65 M NaCitrate pH 5.5, 5.8-8.6 % glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30.3 Å / Num. obs: 31208 / % possible obs: 96.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.4 / % possible all: 78.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.6→30.28 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.36
RfactorNum. reflection% reflection
Rfree0.187 2875 5.05 %
Rwork0.146 --
obs0.148 31208 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 41 279 2112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091987
X-RAY DIFFRACTIONf_angle_d0.9262734
X-RAY DIFFRACTIONf_dihedral_angle_d13.7891210
X-RAY DIFFRACTIONf_chiral_restr0.06300
X-RAY DIFFRACTIONf_plane_restr0.008357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5991-1.62530.4019540.3536995X-RAY DIFFRACTION36
1.6253-1.65330.35511160.29942091X-RAY DIFFRACTION75
1.6533-1.68340.29381210.27642341X-RAY DIFFRACTION87
1.6834-1.71580.32341390.25852512X-RAY DIFFRACTION92
1.7158-1.75080.29471420.23172651X-RAY DIFFRACTION96
1.7508-1.78880.24941350.2152650X-RAY DIFFRACTION96
1.7888-1.83050.261450.19152676X-RAY DIFFRACTION98
1.8305-1.87620.21791430.18122717X-RAY DIFFRACTION99
1.8762-1.92690.23891440.16262675X-RAY DIFFRACTION98
1.9269-1.98360.18681430.1432724X-RAY DIFFRACTION99
1.9836-2.04760.18251420.12832755X-RAY DIFFRACTION100
2.0476-2.12080.1991430.13882715X-RAY DIFFRACTION99
2.1208-2.20570.16221400.1142720X-RAY DIFFRACTION100
2.2057-2.30610.18451450.12292702X-RAY DIFFRACTION99
2.3061-2.42760.1961490.11692769X-RAY DIFFRACTION100
2.4276-2.57960.15441480.12292733X-RAY DIFFRACTION100
2.5796-2.77870.1881420.13492720X-RAY DIFFRACTION100
2.7787-3.0580.17931500.13292768X-RAY DIFFRACTION100
3.058-3.50.17781440.1252719X-RAY DIFFRACTION100
3.5-4.40740.12491440.1212716X-RAY DIFFRACTION99
4.4074-30.2880.16291460.15332747X-RAY DIFFRACTION99

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