[English] 日本語
Yorodumi
- PDB-1bx9: GLUTATHIONE S-TRANSFERASE IN COMPLEX WITH HERBICIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bx9
TitleGLUTATHIONE S-TRANSFERASE IN COMPLEX WITH HERBICIDE
Components
  • FOE-4053-glutathione conjugate GGL-FOE-GLY
  • GLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE/PEPTIDE / HERBICIDE / FOE-4053-glutathione conjugate / product of the detoxifying reaction / TRANSFERASE / TRANSFERASE-PEPTIDE COMPLEX
Function / homology
Function and homology information


response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / auxin-activated signaling pathway / plasmodesma / glutathione binding / plant-type vacuole / apoplast ...response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / auxin-activated signaling pathway / plasmodesma / glutathione binding / plant-type vacuole / apoplast / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / response to cadmium ion / response to cold / chloroplast / peroxidase activity / defense response / protein domain specific binding / intracellular membrane-bounded organelle / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione S-transferase F2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPrade, L. / Huber, R. / Bieseler, B.
CitationJournal: Structure / Year: 1998
Title: Structures of herbicides in complex with their detoxifying enzyme glutathione S-transferase - explanations for the selectivity of the enzyme in plants.
Authors: Prade, L. / Huber, R. / Bieseler, B.
History
DepositionOct 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: FOE-4053-glutathione conjugate GGL-FOE-GLY


Theoretical massNumber of molelcules
Total (without water)24,5322
Polymers24,5322
Non-polymers00
Water1,26170
1
A: GLUTATHIONE S-TRANSFERASE
B: FOE-4053-glutathione conjugate GGL-FOE-GLY

A: GLUTATHIONE S-TRANSFERASE
B: FOE-4053-glutathione conjugate GGL-FOE-GLY


Theoretical massNumber of molelcules
Total (without water)49,0644
Polymers49,0644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)59.000, 88.830, 89.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein GLUTATHIONE S-TRANSFERASE /


Mass: 24031.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P46422
#2: Protein/peptide FOE-4053-glutathione conjugate GGL-FOE-GLY


Mass: 500.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 mMFOE-4053-GSH conjugate1drop
30.1 MHEPES1reservoir
40.1 Mammonium sulfate1reservoir
522.5 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.6→8 Å / Num. obs: 7598 / % possible obs: 97.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.102
Reflection
*PLUS
Redundancy: 2.2 %
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.365

-
Processing

SoftwareName: X-PLOR / Version: 3.8 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 -5 %RANDOM
Rwork0.196 ---
obs0.196 7598 97.8 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 70 1797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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