[English] 日本語
Yorodumi
- PDB-6gsv: FIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gsv
TitleFIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIVE SITE OF A CLASS MU GLUTATHIONE TRANSFERASE
ComponentsMU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / ISOENZYME 3-3 / T13S MUTANT
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 / glutathione transferase / nickel cation binding ...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 / glutathione transferase / nickel cation binding / glutathione transferase activity / response to amino acid / response to axon injury / xenobiotic catabolic process / steroid binding / glutathione metabolic process / response to lead ion / sensory perception of smell / cellular response to xenobiotic stimulus / response to ethanol / response to xenobiotic stimulus / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / identical protein binding / cytosol / cytoplasm
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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...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 Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
Chem-GPS / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsXiao, G. / Ji, X. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1996
Title: First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase.
Authors: Xiao, G. / Liu, S. / Ji, X. / Johnson, W.W. / Chen, J. / Parsons, J.F. / Stevens, W.J. / Gilliland, G.L. / Armstrong, R.N.
#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. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.M. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L.
#2: Journal: J.Am.Chem.Soc. / Year: 1993
Title: Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of ...Title: Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of Tyrosine 6 and its Influence on Catalysis
Authors: Liu, S. / Ji, X. / Gilliland, G.L. / Stevens, W.J. / Armstrong, R.N.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 1992
Title: Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase
Authors: Liu, S. / Zhang, P. / Ji, X. / Johnson, W.W. / Gilliland, G.L. / Armstrong, R.N.
#5: 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-A Resolution
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
History
DepositionJan 26, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3
B: MU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9017
Polymers51,6102
Non-polymers1,2915
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-56 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.620, 68.540, 80.370
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-452-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.83437, -0.0922, 0.54344), (-0.09585, -0.99516, -0.02167), (0.5438, -0.03401, -0.83917)
Vector: -6.38473, 31.80421, 27.03336)

-
Components

#1: Protein MU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3 / RAT GST


Mass: 25804.764 Da / Num. of mol.: 2 / Mutation: T13S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Gene: CDNA INSERT OF CLONE PGT33MX / Organ: LIVER / Plasmid: PGT33MXT13S / Gene (production host): CDNA INSERT OF CLONE PGT33MX / Production host: Escherichia coli (E. coli) / Strain (production host): M5219 / References: UniProt: P04905, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GPS / L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine


Mass: 501.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 47 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-12 mg/mlprotein1drop
225 mMTris-HCl1drop
31 mMEDTA1drop
40.2 %beta-octyl D-glucopyranoside1drop
52 mMproduct inhibitor1drop
640-50 %satammonium sulfate1drop
760-72 %satammonium sulfate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 17, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 45856 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.13 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Num. measured all: 187981

-
Processing

Software
NameClassification
GPRLSArefinement
XENGENdata reduction
XENGENdata scaling
RefinementResolution: 1.75→6 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.181 --
obs-38637 94 %
Displacement parametersBiso mean: 16.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 85 472 4191
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.040.042
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0131
X-RAY DIFFRACTIONp_mcangle_it1.5431.5
X-RAY DIFFRACTIONp_scbond_it1.9411.5
X-RAY DIFFRACTIONp_scangle_it2.7462
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.2410.2
X-RAY DIFFRACTIONp_singtor_nbd0.1950.3
X-RAY DIFFRACTIONp_multtor_nbd0.1850.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_tor4.55
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.315
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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