[English] 日本語
Yorodumi
- PDB-1gum: HUMAN GLUTATHIONE TRANSFERASE A4-4 WITHOUT LIGANDS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gum
TitleHUMAN GLUTATHIONE TRANSFERASE A4-4 WITHOUT LIGANDS
ComponentsPROTEIN (GLUTATHIONE TRANSFERASE A4-4)
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / OXIDATIVE STRESS / ALKENAL DEGRADATION
Function / homology
Function and homology information


Glutathione conjugation / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / protein homodimerization activity / identical protein binding / 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 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. ...Glutathione S-transferase, alpha class / 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-transferase A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBruns, C.M. / Hubatsch, I. / Ridderstrom, M. / Mannervik, B. / Tainer, J.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products
Authors: Bruns, C.M. / Hubatsch, I. / Ridderstrom, M. / Mannervik, B. / Tainer, J.A.
#1: Journal: Biochem.J. / Year: 1998
Title: Human Glutathione Transferase A4-4: An Alpha Class Enzyme with High Catalytic Efficiency in the Conjugation of 4-Hydroxynonenal and Other Genotoxic Products of Lipid Peroxidation
Authors: Hubatsch, I. / Ridderstrom, M. / Mannervik, B.
History
DepositionJun 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.4Aug 9, 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: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
B: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
C: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
D: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
E: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
F: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
G: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
H: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)


Theoretical massNumber of molelcules
Total (without water)205,9058
Polymers205,9058
Non-polymers00
Water3,315184
1
A: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
B: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)


Theoretical massNumber of molelcules
Total (without water)51,4762
Polymers51,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-14 kcal/mol
Surface area19130 Å2
MethodPISA
2
C: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
D: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)


Theoretical massNumber of molelcules
Total (without water)51,4762
Polymers51,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area19050 Å2
MethodPISA
3
E: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
F: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)


Theoretical massNumber of molelcules
Total (without water)51,4762
Polymers51,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-14 kcal/mol
Surface area19110 Å2
MethodPISA
4
G: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)
H: PROTEIN (GLUTATHIONE TRANSFERASE A4-4)


Theoretical massNumber of molelcules
Total (without water)51,4762
Polymers51,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-14 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.300, 156.100, 101.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

-
Components

#1: Protein
PROTEIN (GLUTATHIONE TRANSFERASE A4-4) / E.C.2.5.1.18 / GLUTATHIONE S-TRANSFERASE / GST


Mass: 25738.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: SUBSTANTIA NIGRA / Organ: BRAIN / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O15217, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 100 MM PH 7.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG60001reservoir
2100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC / Detector: CCD / Date: Feb 24, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.9→160 Å / Num. obs: 49774 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rsym value: 0.199 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.48 / % possible all: 97.1
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. obs: 51109 / % possible obs: 92 % / Rmerge(I) obs: 0.118

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSE

1gse


Resolution: 3→160 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2305 5 %RANDOM
Rwork0.253 ---
obs0.255 45948 92 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 476.5 Å2 / ksol: 0.916 e/Å3
Refinement stepCycle: LAST / Resolution: 3→160 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14216 0 0 184 14400
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01818170.8
X-RAY DIFFRACTIONt_angle_deg2.6624431.5
X-RAY DIFFRACTIONt_dihedral_angle_d16.9410850.5
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015481
X-RAY DIFFRACTIONt_gen_planes0.0192533
X-RAY DIFFRACTIONt_it5.6218172
X-RAY DIFFRACTIONt_nbd0.0279610
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.8
X-RAY DIFFRACTIONt_angle_deg1.52.66
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg0.516.94
X-RAY DIFFRACTIONt_planar_d10.015
X-RAY DIFFRACTIONt_plane_restr30.019

+
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