[English] 日本語
Yorodumi
- PDB-8ax2: Crystal structure of Trametes versicolor glutathione transferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ax2
TitleCrystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with glutathione and pentachloro-nitrosyl-osmate
ComponentsGlutathione transferase
KeywordsTRANSFERASE / glutathione transferase / GSTO / detoxification
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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 / OSMIUM ION / Glutathione transferase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsSchwartz, M. / Didierjean, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-LAS-0002-01 France
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural insights into the interactions of glutathione transferases with a nitric oxide carrier and sodium nitroprusside.
Authors: Schwartz, M. / Perrot, T. / Beurton, J. / Zannini, F. / Morel-Rouhier, M. / Gelhaye, E. / Neiers, F. / Schaniel, D. / Favier, F. / Jacquot, J.P. / Leroy, P. / Clarot, I. / Boudier, A. / Didierjean, C.
History
DepositionAug 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2729
Polymers55,0532
Non-polymers1,2197
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-41 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.615, 104.548, 108.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glutathione transferase / Glutathione transferase Omega 3S


Mass: 27526.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes versicolor (turkey-tail fungus)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E145, glutathione transferase

-
Non-polymers , 5 types, 270 molecules

#2: Chemical ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Os / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 30 % PEG 400, 0.2 M Calcium Acetate, 0.1 M Acetate Buffer, pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.14356 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14356 Å / Relative weight: 1
ReflectionResolution: 1.62→50.62 Å / Num. obs: 140484 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Net I/σ(I): 26.9
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 13.3 % / Num. unique obs: 10527 / CC1/2: 0.89 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.62→37.574 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 6883 4.9 %
Rwork0.1846 133601 -
obs0.1858 140484 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.28 Å2 / Biso mean: 20.9174 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: final / Resolution: 1.62→37.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 101 263 4147
Biso mean--27.46 25.49 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063954
X-RAY DIFFRACTIONf_angle_d0.8085376
X-RAY DIFFRACTIONf_chiral_restr0.047572
X-RAY DIFFRACTIONf_plane_restr0.006708
X-RAY DIFFRACTIONf_dihedral_angle_d16.9032364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6201-1.63850.34651580.3147427094
1.6385-1.65780.32482090.26814443100
1.6578-1.6780.26512050.24324510100
1.678-1.69930.2392200.20934416100
1.6993-1.72160.23912410.19064485100
1.7216-1.74520.17911920.18514554100
1.7452-1.77010.21631940.19414436100
1.7701-1.79660.22942330.19514483100
1.7966-1.82460.22562480.19414446100
1.8246-1.85450.23522660.19564401100
1.8545-1.88650.22652470.20644482100
1.8865-1.92080.21332860.19534366100
1.9208-1.95780.22022530.1844490100
1.9578-1.99770.20922210.18244452100
1.9977-2.04120.17322300.17894460100
2.0412-2.08860.23742740.18874449100
2.0886-2.14090.23382160.18494452100
2.1409-2.19870.21892160.17824491100
2.1987-2.26340.19082690.17764426100
2.2634-2.33650.2122510.17564430100
2.3365-2.420.20122410.18694492100
2.42-2.51690.20372550.1914440100
2.5169-2.63140.21471800.19294504100
2.6314-2.77010.21411890.18684494100
2.7701-2.94360.22852000.19794495100
2.9436-3.17070.21932230.20164494100
3.1707-3.48960.21632540.19894413100
3.4896-3.99410.19692630.16264434100
3.9941-5.03020.17042370.15124469100
5.0302-37.5740.17292120.167442499

+
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