[English] 日本語
Yorodumi
- PDB-6gnw: Crystal Structure Of Sea Bream Transthyretin in complex with 2,4,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gnw
TitleCrystal Structure Of Sea Bream Transthyretin in complex with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / 2 / 4 / 5-trichlorophenoxyacetic acid / 5-T
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
2-[2,4,5-tris(chloranyl)phenoxy]ethanoic acid / Transthyretin
Similarity search - Component
Biological speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3316
Polymers57,8204
Non-polymers5112
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-44 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.061, 76.088, 107.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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-F52 / 2-[2,4,5-tris(chloranyl)phenoxy]ethanoic acid


Mass: 255.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5Cl3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. 2,4,5-T was added at 5 x molar excess to the protein. The reservoir contained 28% PEG 4K, 0.1M NaAc ...Details: Purified SaTTR in 100 mM NaCl and 20 mM Tris-HCl, pH 7.5, was concentrated to 5 mg per ml. 2,4,5-T was added at 5 x molar excess to the protein. The reservoir contained 28% PEG 4K, 0.1M NaAc pH 4.5, 0.2M AmAc. Drop size 3 plus 3 microliter

-
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: 1.75→47 Å / Num. obs: 60184 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.049 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

-
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: 1.75→47 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.29
RfactorNum. reflection% reflection
Rfree0.195 2922 4.86 %
Rwork0.159 --
obs0.16 60113 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 28 609 4144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093801
X-RAY DIFFRACTIONf_angle_d0.9865221
X-RAY DIFFRACTIONf_dihedral_angle_d12.8992190
X-RAY DIFFRACTIONf_chiral_restr0.066597
X-RAY DIFFRACTIONf_plane_restr0.008673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77870.27791250.25172675X-RAY DIFFRACTION100
1.7787-1.80940.25661460.23422711X-RAY DIFFRACTION100
1.8094-1.84230.21751360.21972661X-RAY DIFFRACTION100
1.8423-1.87770.23381440.20812696X-RAY DIFFRACTION100
1.8777-1.9160.2421420.2042684X-RAY DIFFRACTION100
1.916-1.95770.17851410.17892700X-RAY DIFFRACTION100
1.9577-2.00320.24061480.17272685X-RAY DIFFRACTION100
2.0032-2.05330.19911470.17942697X-RAY DIFFRACTION100
2.0533-2.10890.25431260.16692679X-RAY DIFFRACTION100
2.1089-2.17090.23451300.15882733X-RAY DIFFRACTION100
2.1709-2.2410.16081400.14782711X-RAY DIFFRACTION100
2.241-2.32110.1821400.14782696X-RAY DIFFRACTION100
2.3211-2.4140.1861320.14972704X-RAY DIFFRACTION100
2.414-2.52390.20311240.14932737X-RAY DIFFRACTION100
2.5239-2.65690.18151370.14822720X-RAY DIFFRACTION100
2.6569-2.82340.14931300.14892765X-RAY DIFFRACTION100
2.8234-3.04130.20311650.15662698X-RAY DIFFRACTION100
3.0413-3.34730.18011020.15242780X-RAY DIFFRACTION100
3.3473-3.83150.17381180.13992816X-RAY DIFFRACTION100
3.8315-4.82650.16281510.12292785X-RAY DIFFRACTION100
4.8265-47.05780.20241980.16212858X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more