[English] 日本語
Yorodumi
- PDB-1gsc: NEW CRYSTAL FORMS OF A MU CLASS GLUTATHIONE S-TRANSFERASE FROM RA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gsc
TitleNEW CRYSTAL FORMS OF A MU CLASS GLUTATHIONE S-TRANSFERASE FROM RAT LIVER
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE(GLUTATHIONE)
Function / homology
Function and homology information


Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase ...Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase / glutathione transferase activity / response to amino acid / xenobiotic catabolic process / response to axon injury / steroid binding / glutathione metabolic process / response to lead ion / cellular response to xenobiotic stimulus / sensory perception of smell / response to ethanol / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / 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, Mu class / Glutathione S-transferase, C-terminal domain / : / 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
Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFu, J.-H. / Rose, J.P. / Wang, B.-C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: New crystal forms of a mu-class glutathione S-transferase from rat liver.
Authors: Fu, J.H. / Rose, J. / Tam, M.F. / Wang, B.C.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Crystals of Isoenzyme 3-3 of Rat Liver Glutathione S-Transferase with and without Inhibitor
Authors: Fu, J.-H. / Rose, J. / Chung, Y.-J. / Tam, M.F. / Wang, B.-C.
History
DepositionSep 8, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)103,2754
Polymers103,2754
Non-polymers00
Water00
1
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)51,6382
Polymers51,6382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)51,6382
Polymers51,6382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.377, 81.109, 69.425
Angle α, β, γ (deg.)90.00, 109.16, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
GLUTATHIONE S-TRANSFERASE / Coordinate model: Cα atoms only


Mass: 25818.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P04905, glutathione transferase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG33501reservoir
2100 mMHEPES1reservoir
310 mMbeta-octylglucopyranoside1drop
40.6 mMethylmercury chloride1drop

-
Processing

RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 0 868

+
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