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- PDB-1ml6: Crystal Structure of mGSTA2-2 in Complex with the Glutathione Con... -

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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 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
#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

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Experimental details

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Experiment

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

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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

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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 %

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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

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