[English] 日本語
Yorodumi
- PDB-1ml6: Crystal Structure of mGSTA2-2 in Complex with the Glutathione Con... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ml6
TitleCrystal Structure of mGSTA2-2 in Complex with the Glutathione Conjugate of Benzo[a]pyrene-7(R),8(S)-Diol-9(S),10(R)-Epoxide
ComponentsGlutathione S-Transferase GT41A
KeywordsTRANSFERASE / GST detoxification / mGSTA2-2
Function / homology
Function and homology information


Heme degradation / Azathioprine ADME / Glutathione conjugation / response to stilbenoid / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to bacterium / mitochondrion / 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
Chem-GBX / ISOPROPYL ALCOHOL / Glutathione S-transferase A2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGu, Y. / Xiao, B. / Wargo, H.L. / Bucher, M.H. / Singh, S.V. / Ji, X.
Citation
Journal: Biochemistry / Year: 2003
Title: Residues 207, 216, and 221 and the catalytic activity of mGSTA1-1 and mGSTA2-2 toward benzo[a]pyrene-(7R,8S)-diol-(9S,10R)-epoxide
Authors: Gu, Y. / Xiao, B. / Wargo, H.L. / Bucher, M.H. / Singh, S.V. / Ji, X.
#1: Journal: Biochemistry / Year: 2000
Title: Residue R216 and Catalytic Efficiency of a Murine Class Alpha Glutathione S-Transferase toward Benzo[a]pyrene 7(R),8(S)-Diol-9(S),10(R)-Epoxide
Authors: Gu, Y. / Singh, S.V. / Ji, X.
#2: Journal: Biochemistry / Year: 1999
Title: Amino Acid Substitutions at Positions 207 and 221 Contribute to Catalytic Differences between Murine Glutathione S-Transferase A1-1 and A2-2 toward (+)-anti-7,8-Dihydroxy-9,10-epoxy-7,8,9,10- ...Title: Amino Acid Substitutions at Positions 207 and 221 Contribute to Catalytic Differences between Murine Glutathione S-Transferase A1-1 and A2-2 toward (+)-anti-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene
Authors: Xia, H. / Gu, Y. / Pan, S.-S. / Ji, X. / Singh, S.V.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-Transferase GT41A
B: Glutathione S-Transferase GT41A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2436
Polymers50,9122
Non-polymers1,3314
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-16 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.067, 93.903, 52.600
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21B-775-

HOH

31B-896-

HOH

-
Components

#1: Protein Glutathione S-Transferase GT41A / GST class-alpha


Mass: 25455.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GST / Plasmid: pET-11d / Production host: Escherichia coli (E. coli) / References: UniProt: P10648, glutathione transferase
#2: Chemical ChemComp-GBX / 2-AMINO-4-[1-(CARBOXYMETHYL-CARBAMOYL)-2-(9-HYDROXY-7,8-DIOXO-7,8,9,10-TETRAHYDRO-BENZO[DEF]CHRYSEN-10-YLSULFANYL)-ETHYLCARBAMOYL]-BUTYRIC ACID / GLUTATHIONE CONJUGATE OF (+)-ANTI-BPDE


Mass: 605.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27N3O9S
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, NaHepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110.0 mg/mlprotein1drop
25-6 %PEG40001drop
33 %2-propanol1drop
420 mMsodium HEPES1droppH7.5
530 %PEG40001reservoir
615 %2-propanol1reservoir
7100 mMsodium HEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1999 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 37794 / Num. obs: 37794 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.038 / Net I/σ(I): 18.68
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.44 / Rsym value: 0.448 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Redundancy: 4.59 %
Reflection shell
*PLUS
% possible obs: 99.2 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3A

1f3a


Resolution: 1.9→26.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1753798.71 / Data cutoff high rms absF: 1753798.71 / 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
Rfree0.2486 1882 5 %RANDOM
Rwork0.2 ---
obs0.2 37774 99.6 %-
all-37774 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9908 Å2 / ksol: 0.335569 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å2-9.3 Å2
2--3.18 Å20 Å2
3----1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 86 334 3986
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it2.531.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it3.892
X-RAY DIFFRACTIONc_scangle_it5.472.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.9-2.020.3273325.30.30859010.018385299.1
2.25-2.39377499.8
2.39-2.58376999.9
2.58-2.84381499.9
2.84-3.253787100
3.25-4.093795100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_1.0.PARAMPROTEIN_1.0.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOPOL
X-RAY DIFFRACTION3PARAM.GBSTOPOL.GBS
X-RAY DIFFRACTION4PRN.PARPRN.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. reflection obs: 35892 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

+
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