[English] 日本語
Yorodumi
- PDB-1gsq: THREE-DIMENSIONAL STRUCTURE, CATALYTIC PROPERTIES AND EVOLUTION O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gsq
TitleTHREE-DIMENSIONAL STRUCTURE, CATALYTIC PROPERTIES AND EVOLUTION OF A SIGMA CLASS GLUTATHIONE TRANSFERASE FROM SQUID, A PROGENITOR OF THE LENS-CRYSTALLINS OF CEPHALOPODS
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
S-crystallin / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...S-crystallin / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE S-(2,4 DINITROBENZENE) / Glutathione S-transferase
Similarity search - Component
Biological speciesOmmastrephes sloani pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJi, X. / Rosenvinge, E.C.V. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1995
Title: Three-dimensional structure, catalytic properties, and evolution of a sigma class glutathione transferase from squid, a progenitor of the lens S-crystallins of cephalopods.
Authors: Ji, X. / von Rosenvinge, E.C. / Johnson, W.W. / Tomarev, S.I. / Piatigorsky, J. / Armstrong, R.N. / Gilliland, G.L.
#1: Journal: Biochemistry / Year: 1994
Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9- ...Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
Authors: Ji, X. / Sesay, M.A. / Dickert, L. / Prassad, S.M. / Johnson, W.W. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L.
#2: Journal: Biochemistry / Year: 1993
Title: Snapshots Along the Reaction Coordinate of an SNAr Reaction Catalyzed by Glutathione Transferase
Authors: Ji, X. / Armstrong, R.N. / Gilliland, G.L.
#3: Journal: Biochemistry / Year: 1992
Title: The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2 Angstroms Resolution
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
History
DepositionJan 9, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software / Item: _pdbx_database_status.process_site / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2942
Polymers22,8211
Non-polymers4731
Water2,774154
1
A: GLUTATHIONE S-TRANSFERASE
hetero molecules

A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5884
Polymers45,6412
Non-polymers9472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4490 Å2
ΔGint-25 kcal/mol
Surface area17830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.760, 72.760, 94.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO 51
2: RESIDUE 203: ATOMS SG2, C1', C2', C3', C4', C5',C6', N2', O21, O22, N4', O41 AND O42 HAVE OCCUPANCY OF 0.70.
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 203 TO FORM THE BIOLOGICALLY ACTIVE DIMERIC MOLECULE, THE SECOND MONOMER NEEDS TO BE GENERATED BY USING THE FOLLOWING MATRIX. SYMMETRY1 1 -0.499940 0.866060 -0.000030 -0.00159 SYMMETRY2 1 0.866060 0.499940 -0.000030 0.00002 SYMMETRY3 1 -0.000010 -0.000040 -1.000000 0.00153

-
Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 22820.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ommastrephes sloani pacificus (Japanese flying squid)
Species: Ommastrephes sloani / Strain: pacificus / Gene: CDNA INSERT OF CLONE PGST5 / Organ: DIGESTIVE GLAND / Plasmid: GST5/PET / Gene (production host): CDNA INSERT OF CLONE PGST5 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P46088, glutathione transferase
#2: Chemical ChemComp-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE)


Mass: 473.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N5O10S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-8 mg/mlprotein1drop
225 mMTris-HCl1drop
31 mMEDTA1drop
42 mM1-(S-glutathionyl)-2,4-dinitrobenzene1drop
540 %satammonium sulfate1drop
660-70 %satammonium sulfate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ELECTRONICS COMPUTING TECHNOLOGIES / Detector: AREA DETECTOR / Date: Jan 11, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11745 / % possible obs: 99.7 % / Redundancy: 3.84 %
Reflection
*PLUS
Highest resolution: 2.4 Å / Rmerge(I) obs: 0.087

-
Processing

Software
NameClassification
GPRLSArefinement
PROLSQrefinement
XENGENdata reduction
RefinementResolution: 2.4→6 Å / σ(F): 4 /
RfactorNum. reflection% reflection
obs0.18 8302 75 %
Displacement parametersBiso mean: 27.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 32 154 1784
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.025
X-RAY DIFFRACTIONp_angle_d0.0360.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.551
X-RAY DIFFRACTIONp_mcangle_it0.9421.5
X-RAY DIFFRACTIONp_scbond_it0.8881.5
X-RAY DIFFRACTIONp_scangle_it1.3712
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.2210.2
X-RAY DIFFRACTIONp_singtor_nbd0.2050.3
X-RAY DIFFRACTIONp_multtor_nbd0.220.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.55
X-RAY DIFFRACTIONp_staggered_tor22.415
X-RAY DIFFRACTIONp_orthonormal_tor25.915
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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