[English] 日本語
Yorodumi
- PDB-1fw1: Glutathione transferase zeta/maleylacetoacetate isomerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fw1
TitleGlutathione transferase zeta/maleylacetoacetate isomerase
ComponentsGLUTATHIONE TRANSFERASE ZETA
KeywordsISOMERASE/TRANSFERASE / glutathione transferase / ISOMERASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


maleylacetoacetate isomerase / Tyrosine catabolism / maleylacetoacetate isomerase activity / Regulation of pyruvate dehydrogenase (PDH) complex / L-tyrosine catabolic process / Glutathione conjugation / glutathione peroxidase activity / L-phenylalanine catabolic process / cellular detoxification / glutathione transferase ...maleylacetoacetate isomerase / Tyrosine catabolism / maleylacetoacetate isomerase activity / Regulation of pyruvate dehydrogenase (PDH) complex / L-tyrosine catabolic process / Glutathione conjugation / glutathione peroxidase activity / L-phenylalanine catabolic process / cellular detoxification / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrial matrix / protein homodimerization activity / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / GLUTATHIONE / Maleylacetoacetate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsPolekhina, G. / Board, P.G. / Blackburn, A.C. / Parker, M.W.
Citation
Journal: Biochemistry / Year: 2001
Title: Crystal structure of maleylacetoacetate isomerase/glutathione transferase zeta reveals the molecular basis for its remarkable catalytic promiscuity.
Authors: Polekhina, G. / Board, P.G. / Blackburn, A.C. / Parker, M.W.
#1: Journal: Cytogenet.Cell Genet. / Year: 1998
Title: Characterization and chromosome location of the gene GSTZ1 encoding the human Zeta class glutathione transferase and maleylacetoacetate isomerase
Authors: Blackburn, A.C. / Woollatt, E. / Sutherland, G.R. / Board, P.G.
#2: Journal: Biochem.J. / Year: 1998
Title: Glutathione transferase Zeta catalyses the oxygenation of the carcinogen dichloroacetic acid to glyoxylic acid
Authors: Tong, Z. / Board, P.G. / Anders, M.W.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 TRANSFERASE ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6664
Polymers24,1081
Non-polymers5583
Water1,964109
1
A: GLUTATHIONE TRANSFERASE ZETA
hetero molecules

A: GLUTATHIONE TRANSFERASE ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3318
Polymers48,2162
Non-polymers1,1156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5640 Å2
ΔGint-91 kcal/mol
Surface area16970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.000, 100.000, 56.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

21A-327-

HOH

DetailsThe biological assembly is a dimer. The dimer can be created from monomer A through the crystallographic 2-fold axis. The symmetry operation to be used is y,x,-z.

-
Components

#1: Protein GLUTATHIONE TRANSFERASE ZETA / MALEYLACETOACETATE ISOMERASE


Mass: 24107.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O43708, maleylacetoacetate isomerase, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: ammonium sulfate, tert-butanol, bicine, glutathione, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K, temperature 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMHEPES1drop
22 mMdithiothreitol1drop
32 mMGSH1drop
410 mg/mlprotein1drop
5100 mMBicine1reservoir
610 mMdithiothreitol1reservoir
710 mMGSH1reservoir
848-52 %satammonium sulfate1reservoir
91 %tert-butyl alcohol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 22750 / Num. obs: 152479 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.286 / Num. unique all: 1340 / % possible all: 88.7
Reflection
*PLUS
Num. obs: 22750 / Num. measured all: 152479
Reflection shell
*PLUS
Mean I/σ(I) obs: 7.4

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→28.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1875438.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2317 10.2 %RANDOM
Rwork0.234 ---
all0.234 22697 --
obs0.234 22697 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.05 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--17.76 Å20 Å20 Å2
2---17.76 Å20 Å2
3---35.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 33 109 1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.322.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 341 10.3 %
Rwork0.439 2977 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GSH_1.PARGSH_1.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.463 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.439

+
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