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- PDB-6gnr: Crystal Structure Of Sea Bream Transthyretin in complex with 2-(3... -

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Basic information

Entry
Database: PDB / ID: 6gnr
TitleCrystal Structure Of Sea Bream Transthyretin in complex with 2-(3-chloro-2-methylanilino)pyridine-3-carboxylic acid (Clonixin)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / 2-(3-chloro-2-methylanilino)pyridine-3-carboxylic acid / clonixin
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
Chem-6J3 / Transthyretin
Similarity search - Component
Biological speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4364
Polymers28,9102
Non-polymers5252
Water6,521362
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8718
Polymers57,8204
Non-polymers1,0514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)59.678, 59.678, 115.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-201-

6J3

21B-486-

HOH

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Components

#1: Protein Transthyretin


Mass: 14455.096 Da / Num. of mol.: 2
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-6J3 / 2-(3-chloro-2-methylanilino)pyridine-3-carboxylic acid


Mass: 262.692 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11ClN2O2 / Comment: antiinflammatory, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. Clonixin was added at 5 x molar excess to the protein. The reservoir contained 2 M AmSO4, 0.1 M ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. Clonixin was added at 5 x molar excess to the protein. The reservoir contained 2 M AmSO4, 0.1 M NaAc, pH 4.6. 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: 1.4→47.2 Å / Num. obs: 47720 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.1
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2484 / % possible all: 99.6

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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: 1.4→47.189 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.57
RfactorNum. reflection% reflection
Rfree0.1721 2314 4.85 %
Rwork0.1363 --
obs0.138 47670 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 36 362 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081947
X-RAY DIFFRACTIONf_angle_d0.9712682
X-RAY DIFFRACTIONf_dihedral_angle_d17.355672
X-RAY DIFFRACTIONf_chiral_restr0.089302
X-RAY DIFFRACTIONf_plane_restr0.008349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42860.23871280.17892626X-RAY DIFFRACTION99
1.4286-1.45970.28251500.19342615X-RAY DIFFRACTION99
1.4597-1.49360.21061570.17262601X-RAY DIFFRACTION99
1.4936-1.5310.19461110.15372659X-RAY DIFFRACTION100
1.531-1.57240.16641520.13082597X-RAY DIFFRACTION100
1.5724-1.61870.17411220.12122650X-RAY DIFFRACTION100
1.6187-1.67090.17971010.12352663X-RAY DIFFRACTION100
1.6709-1.73060.19291670.12382623X-RAY DIFFRACTION100
1.7306-1.79990.19061460.12882622X-RAY DIFFRACTION100
1.7999-1.88180.18281410.12672668X-RAY DIFFRACTION100
1.8818-1.9810.15561180.11642682X-RAY DIFFRACTION100
1.981-2.10520.16831120.12152701X-RAY DIFFRACTION100
2.1052-2.26770.15231450.11582643X-RAY DIFFRACTION100
2.2677-2.49590.16771270.12242707X-RAY DIFFRACTION100
2.4959-2.8570.16051230.13812719X-RAY DIFFRACTION100
2.857-3.59940.17441740.13842698X-RAY DIFFRACTION100
3.5994-47.21560.15121400.15292882X-RAY DIFFRACTION100

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