[English] 日本語
Yorodumi
- PDB-7db0: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7db0
TitleCrystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in dimedone-bound form
ComponentsGlutathione S-transferase E14
KeywordsTRANSFERASE / Drosophila melanogaster / Glutathione S-transferase / GST / GSTE14 / Inhibitor / Ecdysteroid
Function / homology
Function and homology information


ecdysteroid biosynthetic process / steroid Delta-isomerase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cholesterol homeostasis / response to toxic substance / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
5,5-DIMETHYLCYCLOHEXANE-1,3-DIONE / Glutathione S-transferase E14
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKoiwai, K. / Inaba, K. / Yumoto, F. / Senda, T. / Niwa, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)18am0101113j0002 Japan
Japan Society for the Promotion of Science (JSPS)15K14719 Japan
Japan Society for the Promotion of Science (JSPS)18K19163 Japan
CitationJournal: J Pestic Sci / Year: 2021
Title: Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo
Authors: Koiwai, K. / Morohashi, K. / Inaba, K. / Ebihara, K. / Kojima, H. / Okabe, T. / Yoshino, R. / Hirokawa, T. / Nampo, T. / Fujikawa, Y. / Inoue, H. / Yumoto, F. / Senda, T. / Niwa, R.
History
DepositionOct 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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: Glutathione S-transferase E14
B: Glutathione S-transferase E14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,30516
Polymers55,0882
Non-polymers1,21814
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint9 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.253, 74.747, 109.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Glutathione S-transferase E14 / Protein noppera-bo


Mass: 27543.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstE14, GSTD14-14, nobo, CG4688 / Plasmid: pCOLD_III / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7JYX0, glutathione transferase
#2: Chemical ChemComp-DC1 / 5,5-DIMETHYLCYCLOHEXANE-1,3-DIONE / 2,2 DIMETHYL,1,6 CYCLOHEXA DIONE / DIMEDONE


Mass: 140.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 34% (v/v) PPG400 in 80mM Bis-Tris, pH 6.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→35.39 Å / Num. obs: 56430 / % possible obs: 99.86 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.98 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.057 / Rrim(I) all: 0.128 / Net I/σ(I): 11.6
Reflection shellResolution: 1.66→1.719 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5570 / CC1/2: 0.721 / CC star: 0.915 / Rpim(I) all: 0.3663 / Rrim(I) all: 0.82 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSJun 17, 2015data reduction
Aimless0.5.15data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KEM

6kem


Resolution: 1.66→35.39 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 2904 5.15 %
Rwork0.1721 53523 -
obs0.1736 56427 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.22 Å2
Refinement stepCycle: LAST / Resolution: 1.66→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 68 523 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543855
X-RAY DIFFRACTIONf_angle_d0.71685240
X-RAY DIFFRACTIONf_chiral_restr0.215578
X-RAY DIFFRACTIONf_plane_restr0.004685
X-RAY DIFFRACTIONf_dihedral_angle_d23.35381428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.23781430.24092533X-RAY DIFFRACTION99.93
1.69-1.720.25341400.22792467X-RAY DIFFRACTION99.96
1.72-1.750.27131390.22472532X-RAY DIFFRACTION99.93
1.75-1.780.24331220.22172536X-RAY DIFFRACTION99.96
1.78-1.820.26371360.22092502X-RAY DIFFRACTION99.92
1.82-1.860.25511330.21062528X-RAY DIFFRACTION99.96
1.86-1.90.21791550.20622510X-RAY DIFFRACTION99.96
1.9-1.950.25561510.19072496X-RAY DIFFRACTION100
1.95-20.20951490.18762531X-RAY DIFFRACTION99.96
2-2.060.1941330.16962523X-RAY DIFFRACTION99.96
2.06-2.130.18951450.17272524X-RAY DIFFRACTION99.96
2.13-2.20.18641410.16582546X-RAY DIFFRACTION99.89
2.2-2.290.1981310.16612563X-RAY DIFFRACTION99.89
2.29-2.390.21251120.15942546X-RAY DIFFRACTION99.92
2.39-2.520.20381340.16932542X-RAY DIFFRACTION99.96
2.52-2.680.18641670.1652542X-RAY DIFFRACTION99.96
2.68-2.880.21991160.16682587X-RAY DIFFRACTION99.96
2.88-3.170.17091320.16072580X-RAY DIFFRACTION99.93
3.17-3.630.19091400.15152585X-RAY DIFFRACTION99.71
3.63-4.580.17681470.13922609X-RAY DIFFRACTION99.53
4.58-35.390.17791380.1752741X-RAY DIFFRACTION99.24

+
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