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- PDB-6gnm: Crystal Structure Of Sea Bream Transthyretin in complex with 2,2'... -

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Basic information

Entry
Database: PDB / ID: 6gnm
TitleCrystal Structure Of Sea Bream Transthyretin in complex with 2,2',4,4'-tetrahydroxybenzophenone (BP2)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine disrupting chemicals / TDCs / 2 / 2' / 4 / 4'-tetrahydroxybenzophenone / BP2
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
bis(2,4-dihydroxyphenyl)methanone / Transthyretin
Similarity search - Component
Biological speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 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)58,3136
Polymers57,8204
Non-polymers4922
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-45 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.526, 75.845, 107.552
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-27M / bis(2,4-dihydroxyphenyl)methanone


Mass: 246.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
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. BP2 was added at 5 x molar excess to the protein. The reservoir contained 0.01M ZnSO4 hepahyrate, 0. ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. BP2 was added at 5 x molar excess to the protein. The reservoir contained 0.01M ZnSO4 hepahyrate, 0.1M MES pH 6.5, 25% PEG-MME 550. Drop size 3 plus 3 microliter

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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: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.24→59.56 Å / Num. obs: 27586 / % possible obs: 95.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.8
Reflection shellResolution: 2.24→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.3 / % possible all: 81.6

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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: 1SN2

1sn2


Resolution: 2.24→59.56 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.56
RfactorNum. reflection% reflection
Rfree0.253 2436 4.99 %
Rwork0.179 --
obs0.183 27586 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.24→59.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 36 325 3862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043748
X-RAY DIFFRACTIONf_angle_d0.65147
X-RAY DIFFRACTIONf_dihedral_angle_d10.5632175
X-RAY DIFFRACTIONf_chiral_restr0.049588
X-RAY DIFFRACTIONf_plane_restr0.004657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2381-2.28380.301940.25451767X-RAY DIFFRACTION59
2.2838-2.33340.3111410.25282389X-RAY DIFFRACTION79
2.3334-2.38770.30661340.25112501X-RAY DIFFRACTION81
2.3877-2.44740.28811220.24922430X-RAY DIFFRACTION80
2.4474-2.51360.28521250.23922534X-RAY DIFFRACTION84
2.5136-2.58760.30761400.2382623X-RAY DIFFRACTION86
2.5876-2.67110.30271430.24562651X-RAY DIFFRACTION87
2.6711-2.76660.32291410.22282690X-RAY DIFFRACTION89
2.7666-2.87730.31151510.21842781X-RAY DIFFRACTION91
2.8773-3.00830.29791520.20442878X-RAY DIFFRACTION95
3.0083-3.16690.25581570.19213018X-RAY DIFFRACTION99
3.1669-3.36530.29751650.18583003X-RAY DIFFRACTION98
3.3653-3.62510.2851530.16683015X-RAY DIFFRACTION99
3.6251-3.98980.24041610.15113045X-RAY DIFFRACTION99
3.9898-4.5670.18131490.12473014X-RAY DIFFRACTION100
4.567-5.75310.17731460.11343074X-RAY DIFFRACTION100
5.7531-59.57910.1921620.16483013X-RAY DIFFRACTION99

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