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- PDB-6gon: Crystal Structure Of Sea Bream Transthyretin in complex with Perf... -

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Basic information

Entry
Database: PDB / ID: 6gon
TitleCrystal Structure Of Sea Bream Transthyretin in complex with Perfluorooctanoic acid (PFOA). Crystallized in PEG
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / Perfluorooctanoic acid / PFOA
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
pentadecafluorooctanoic acid / Transthyretin
Similarity search - Component
Biological speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1, 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 / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,6496
Polymers57,8204
Non-polymers8282
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-41 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.408, 76.203, 107.103
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-8PF / pentadecafluorooctanoic acid


Mass: 414.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8HF15O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
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. PFOA was added at 5 x molar excess to the protein. The reservoir contained 18% PEG 8K, 0.1M Na ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. PFOA was added at 5 x molar excess to the protein. The reservoir contained 18% PEG 8K, 0.1M Na Cacodylate pH 6.5, 0.2M CaAc. 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: 1.65→47.1 Å / Num. obs: 71898 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 2 / Num. unique obs: 3605 / % possible all: 99.9

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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: 1.65→43.814 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.15
RfactorNum. reflection% reflection
Rfree0.1927 3615 5.03 %
Rwork0.1591 --
obs0.1608 71818 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 50 560 4098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093836
X-RAY DIFFRACTIONf_angle_d1.1955322
X-RAY DIFFRACTIONf_dihedral_angle_d14.0892214
X-RAY DIFFRACTIONf_chiral_restr0.069603
X-RAY DIFFRACTIONf_plane_restr0.008664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67170.25331260.24792581X-RAY DIFFRACTION100
1.6717-1.69460.21871530.22762587X-RAY DIFFRACTION100
1.6946-1.71880.24131430.21862559X-RAY DIFFRACTION100
1.7188-1.74450.27461260.20552615X-RAY DIFFRACTION100
1.7445-1.77180.24031620.2052566X-RAY DIFFRACTION100
1.7718-1.80080.24941590.20112573X-RAY DIFFRACTION100
1.8008-1.83190.21551470.19092567X-RAY DIFFRACTION100
1.8319-1.86520.21261460.18642593X-RAY DIFFRACTION100
1.8652-1.9010.22131310.17922633X-RAY DIFFRACTION100
1.901-1.93980.19831320.16212593X-RAY DIFFRACTION100
1.9398-1.9820.17141390.15332602X-RAY DIFFRACTION100
1.982-2.02810.16811410.16062593X-RAY DIFFRACTION100
2.0281-2.07880.21611140.16622626X-RAY DIFFRACTION100
2.0788-2.13510.20181080.15482642X-RAY DIFFRACTION100
2.1351-2.19790.16971600.14762597X-RAY DIFFRACTION100
2.1979-2.26880.20441250.14552640X-RAY DIFFRACTION100
2.2688-2.34990.14971180.14662629X-RAY DIFFRACTION100
2.3499-2.4440.17531420.15192620X-RAY DIFFRACTION100
2.444-2.55520.21621530.14662607X-RAY DIFFRACTION100
2.5552-2.68990.17411510.15332627X-RAY DIFFRACTION100
2.6899-2.85840.17131350.15062627X-RAY DIFFRACTION100
2.8584-3.0790.19581590.15542629X-RAY DIFFRACTION100
3.079-3.38880.18081260.14652675X-RAY DIFFRACTION100
3.3888-3.87890.17671250.14462697X-RAY DIFFRACTION100
3.8789-4.8860.1751450.12922702X-RAY DIFFRACTION100
4.886-43.82990.20751490.17542823X-RAY DIFFRACTION99

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