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- PDB-6gnp: Crystal Structure Of Sea Bream Transthyretin in complex with 3,5,... -

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Basic information

Entry
Database: PDB / ID: 6gnp
TitleCrystal Structure Of Sea Bream 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


thyroid hormone binding / purine nucleobase metabolic process / hormone activity / extracellular region
Similarity search - Function
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 speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 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
DepositionMay 31, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2176
Polymers57,8204
Non-polymers3972
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-46 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.171, 75.929, 107.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transthyretin


Mass: 14455.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sparus aurata (gilthead seabream) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTT3
#2: Chemical ChemComp-F4Z / 3,5,6-trichloro-2-pyridinol


Mass: 198.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H2Cl3NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. TC2P was added at 5 x molar excess to the protein. The reservoir contained 30% PEG 8K, 0.1M ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. TC2P was added at 5 x molar excess to the protein. The reservoir contained 30% PEG 8K, 0.1M NaCacodylate pH 6.5, 0.2M AmSO4. Drop size 3 plus 3 microliter

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→46.7 Å / Num. obs: 38625 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2704 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sn2

1sn2


Resolution: 2.019→46.7 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.2191 1873 4.86 %
Rwork0.1744 --
obs0.1766 38559 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.019→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 20 367 3869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123652
X-RAY DIFFRACTIONf_angle_d1.1185005
X-RAY DIFFRACTIONf_dihedral_angle_d14.8872096
X-RAY DIFFRACTIONf_chiral_restr0.067581
X-RAY DIFFRACTIONf_plane_restr0.008634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0195-2.07410.31681370.26112676X-RAY DIFFRACTION96
2.0741-2.13510.2551540.22512772X-RAY DIFFRACTION100
2.1351-2.2040.23421380.19922783X-RAY DIFFRACTION100
2.204-2.28280.26491410.19612794X-RAY DIFFRACTION100
2.2828-2.37420.29711600.19492823X-RAY DIFFRACTION100
2.3742-2.48230.28551130.20262817X-RAY DIFFRACTION100
2.4823-2.61310.22711060.19592858X-RAY DIFFRACTION100
2.6131-2.77680.2281650.19012765X-RAY DIFFRACTION100
2.7768-2.99120.25971780.18642814X-RAY DIFFRACTION100
2.9912-3.29210.24491460.17722827X-RAY DIFFRACTION100
3.2921-3.76830.19011540.1492845X-RAY DIFFRACTION100
3.7683-4.7470.15171470.12972895X-RAY DIFFRACTION100
4.747-46.72940.17171340.15553017X-RAY DIFFRACTION99

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