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- PDB-1b48: CRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-... -

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Basic information

Entry
Database: PDB / ID: 1b48
TitleCRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-HYDROXYNONENAL IN ONE SUBUNIT AND GSH IN THE OTHER: EVIDENCE OF SIGNALING ACROSS DIMER INTERFACE IN MGSTA4-4
ComponentsPROTEIN (GLUTATHIONE S-TRANSFERASE)
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / GST / SUBUNIT COOPERATIVITY
Function / homology
Function and homology information


organic cyclic compound binding / glutathione transferase / glutathione transferase activity / toxic substance binding / xenobiotic metabolic process / glutathione metabolic process / cytoplasm
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 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 / 4-S-GLUTATHIONYL-5-PENTYL-TETRAHYDRO-FURAN-2-OL / Glutathione S-transferase A4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXiao, B. / Zimniak, P. / Ji, X.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structure of a murine glutathione S-transferase in complex with a glutathione conjugate of 4-hydroxynon-2-enal in one subunit and glutathione in the other: evidence of signaling across the dimer interface.
Authors: Xiao, B. / Singh, S.P. / Nanduri, B. / Awasthi, Y.C. / Zimniak, P. / Ji, X.
#1: Journal: FEBS Lett. / Year: 1998
Title: Crystal Structure of a Murine Alpha-Class Glutathione S-Transferase Involved in Cellular Defense Against Oxidative Stress
Authors: Krengel, U. / Schroter, K.H. / Hoier, H. / Arkema, A. / Kalk, K.H. / Zimniak, P. / Dijkstra, B.W.
History
DepositionJan 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7244
Polymers50,9532
Non-polymers7712
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-33 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.450, 96.140, 50.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99956, -0.016641, -0.024543), (-0.016804, -0.364064, 0.931222), (-0.024432, 0.931225, 0.363625)
Vector: 76.44717, 9.54691, -5.14296)

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Components

#1: Protein PROTEIN (GLUTATHIONE S-TRANSFERASE) / GST / MGSTA4-4


Mass: 25476.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: CYTOPLASM / Organ: LUNG / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / Variant (production host): PET9A/MGSTA4 / References: UniProt: P24472, glutathione transferase
#2: Chemical ChemComp-HAG / 4-S-GLUTATHIONYL-5-PENTYL-TETRAHYDRO-FURAN-2-OL / GSHNA


Mass: 463.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H33N3O8S
#3: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 0.11 MM PROTEIN IN 0.047 M HEPES BUFFER (PH 7.5) CONTAINING 1.82 MM GLUTATHIONE, 10.91 MM HNA-SG (GSH CONJUGATE OF 4- ...Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 0.11 MM PROTEIN IN 0.047 M HEPES BUFFER (PH 7.5) CONTAINING 1.82 MM GLUTATHIONE, 10.91 MM HNA-SG (GSH CONJUGATE OF 4-HYDROXYNONENAL), 9.1% ETHANOL, 4.5% ISOPROPANOL, AND 6.5% PEG MONOMETHYL ETHER 5K (PH 7.5). THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING 10% ISOPROPANOL AND 12% PEG MONOMETHYL ETHER 5K IN 80 MM HEPES BUFFER (PH 7.5).
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18-20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.11 mMprotein1drop
21.8 mMGSH1drop
33.6 mMHEPES1drop
55.5 %2-propanol1drop
66.5 %mPEG50001drop
70.044 MHEPES1drop
810 %2-propanol1reservoir
912 %mPEG50001reservoir
4ethanol1drop1ml
100.08 MHEPES1reservoir
1111 mMGSHna1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 15647 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.35 / % possible all: 60.1
Reflection shell
*PLUS
% possible obs: 60.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUH

1guh


Resolution: 2.6→20 Å / Data cutoff high absF: 20 / Data cutoff low absF: 2.6 / Cross valid method: FREE R / σ(F): 2 / Details: ALL DATA WERE INCLUDED IN MAP CALCULATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 781 5 %RANDOM
Rwork0.244 ---
obs0.244 15647 87.4 %-
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 51 40 3677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.364
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.117
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3589 73 3.336 %
Rwork0.3328 1251 -
obs--60.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.117

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