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- PDB-1m0u: Crystal Structure of the Drosophila Glutathione S-transferase-2 i... -

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Basic information

Entry
Database: PDB / ID: 1m0u
TitleCrystal Structure of the Drosophila Glutathione S-transferase-2 in Complex with Glutathione
ComponentsGST2 gene product
KeywordsTRANSFERASE / GST / Flight Muscle Protein / Sigma
Function / homology
Function and homology information


Glutathione conjugation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-D synthase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / 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, C-terminal domain / : / 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 / Glutathione S-transferase S1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.75 Å
AuthorsAgianian, B. / Tucker, P.A. / Schouten, A. / Leonard, K. / Bullard, B. / Gros, P.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structure of a Drosophila Sigma Class Glutathione S-transferase Reveals a Novel Active Site Topography Suited for Lipid Peroxidation Products
Authors: Agianian, B. / Tucker, P.A. / Schouten, A. / Leonard, K. / Bullard, B. / Gros, P.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Catalytic function of Drosophila melanogaster glutathione S-transferase DmGSTS1-1 (GST-2) in conjuction of lipid peroxidation end products
Authors: Singh, S.P. / Coronella, J.A. / Benes, H. / Cochrane, B.J. / Zimniak, P.
History
DepositionJun 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2012Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GST2 gene product
B: GST2 gene product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7805
Polymers55,2812
Non-polymers4993
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-45 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.723, 89.723, 131.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains the biological dimer

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Components

#1: Protein GST2 gene product / Glutathione S-transferase-2


Mass: 27640.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P41043, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 304 / 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: 2.77 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, Sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7 / Details: Agianian, B., (2001) Acta Crystallogr., D57, 725.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
220 mMsodium phosphate1droppH7.0
32 mMbeta-mercaptoethanol1drop
415 mMGSH1drop
51.6-1.9 Mammonium sulfate1reservoir
60.1 Msodium phosphate1reservoirpH6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.75→76.7 Å / Num. all: 62202 / Num. obs: 62202 / % possible obs: 99.5 % / Rsym value: 0.039
Reflection shellResolution: 1.75→1.78 Å / Rsym value: 0.238 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 623131 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 9.14

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1.19refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIRAS / Resolution: 1.75→70 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.202 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23167 6116 9.8 %RANDOM
Rwork0.21272 ---
obs0.21462 56042 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 30 304 3614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223387
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9744606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7945404
X-RAY DIFFRACTIONr_chiral_restr0.0820.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022544
X-RAY DIFFRACTIONr_nbd_refined0.2060.21647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.216
X-RAY DIFFRACTIONr_mcbond_it0.7431.52032
X-RAY DIFFRACTIONr_mcangle_it1.39823306
X-RAY DIFFRACTIONr_scbond_it1.99931355
X-RAY DIFFRACTIONr_scangle_it3.334.51300
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 485
Rwork0.271 4084
Refinement
*PLUS
Lowest resolution: 70 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.19

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