[English] 日本語
Yorodumi
- PDB-6ato: Crystal structure of hGSTA1-1 complexed with GSH and MPD in each ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ato
TitleCrystal structure of hGSTA1-1 complexed with GSH and MPD in each subunit
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / Glutathione S-transferase / glutathione transferase / GST / hGSTA1-1 / GSH
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid Delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid Delta-isomerase activity / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / epithelial cell differentiation / glutathione metabolic process / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, alpha class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
GLUTATHIONE / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsKumari, V. / Ji, X.
Citation
Journal: To be published
Title: The dynamic nature of hGSTA1-1 C-terminal helix
Authors: Kumari, V. / Ji, X.
#1: Journal: J. Mol. Biol. / Year: 1993
Title: Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes.
Authors: Sinning, I. / Kleywegt, G.J. / Cowan, S.W. / Reinemer, P. / Dirr, H.W. / Huber, R. / Gilliland, G.L. / Armstrong, R.N. / Ji, X. / Board, P.G.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,52011
Polymers51,0782
Non-polymers1,4429
Water10,269570
1
A: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3196
Polymers25,5391
Non-polymers7805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2015
Polymers25,5391
Non-polymers6624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.675, 90.960, 50.751
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21A-614-

HOH

31B-522-

HOH

41B-602-

HOH

51B-647-

HOH

61B-667-

HOH

-
Components

#1: Protein Glutathione S-transferase A1 / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1


Mass: 25538.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pET30b(+)/hGSTA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.23 Å3/Da / Density % sol: 44.89 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 200 MME, 25% (w/v), 0.1 M Tris HCl, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 63121 / % possible obs: 97.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.22
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 2.15 / Num. unique all: 5935 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GUH

1guh


Resolution: 1.55→28.976 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.93
RfactorNum. reflection% reflection
Rfree0.2079 1033 1.64 %
Rwork0.1695 --
obs0.1701 63095 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→28.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 96 570 4244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053803
X-RAY DIFFRACTIONf_angle_d0.8295127
X-RAY DIFFRACTIONf_dihedral_angle_d11.0422384
X-RAY DIFFRACTIONf_chiral_restr0.049557
X-RAY DIFFRACTIONf_plane_restr0.017641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5466-1.62810.28611420.22798218X-RAY DIFFRACTION90
1.6281-1.73010.25721370.21279082X-RAY DIFFRACTION100
1.7301-1.86370.22541640.18669122X-RAY DIFFRACTION100
1.8637-2.05120.21361620.17039095X-RAY DIFFRACTION100
2.0512-2.34790.22191300.16239101X-RAY DIFFRACTION99
2.3479-2.95760.18781530.17458878X-RAY DIFFRACTION97
2.9576-28.98070.19371450.15228566X-RAY DIFFRACTION92

+
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