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- PDB-4png: Glutathione S-transferase from Drosophila melanogaster - isozyme E7 -

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Basic information

Entry
Database: PDB / ID: 4png
TitleGlutathione S-transferase from Drosophila melanogaster - isozyme E7
ComponentsLD04004p
KeywordsTRANSFERASE / glutathione S-transferase / isozyme / epsilon class
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / 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 domain / Glutathione S-transferase, C-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 / 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
L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / Glutathione S transferase E7 / LD04004p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 Å
AuthorsScian, M. / Le Trong, I. / Mannervik, B. / Atkins, W.M. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Comparison of epsilon- and delta-class glutathione S-transferases: the crystal structures of the glutathione S-transferases DmGSTE6 and DmGSTE7 from Drosophila melanogaster.
Authors: Scian, M. / Le Trong, I. / Mazari, A.M. / Mannervik, B. / Atkins, W.M. / Stenkamp, R.E.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LD04004p
B: LD04004p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4174
Polymers52,7382
Non-polymers6792
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-19 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.731, 87.090, 87.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LD04004p


Mass: 26368.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstE7, CG17531 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MR33, UniProt: A1ZB72*PLUS
#2: Chemical ChemComp-GSF / L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / GLUTATHIONE SULFINATE


Mass: 339.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHORS STATE THAT DENSITY IS OBSERVED FOR ONLY ONE OF THE OXYGEN ATOMS OF THE SULFINIC GROUP OF LIGAND GSF.

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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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris HCl pH 7.5, 25% w/v PEG4000, 2 mM GSH, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.53→34.58 Å / Num. obs: 63530 / % possible obs: 96.5 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.024 / Net I/σ(I): 21.1 / Num. measured all: 285608
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.53-1.562.90.3722.9512917790.8280.23855.8
8.38-34.584.40.01382.1194844410.00795.4

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Processing

Software
NameVersionClassification
XDS0.1.26data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
Aimlessdata scaling
RefinementResolution: 1.53→34.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.242 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 3223 5.1 %RANDOM
Rwork0.1584 60244 --
obs0.16 63467 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 15.377 Å2 / Biso min: 6.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20 Å2
2---0.38 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.53→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 42 403 4022
Biso mean--11.2 22.22 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193742
X-RAY DIFFRACTIONr_bond_other_d0.0010.023536
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.975079
X-RAY DIFFRACTIONr_angle_other_deg1.89738141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06724.078179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0715622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.351519
X-RAY DIFFRACTIONr_chiral_restr0.1230.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02885
X-RAY DIFFRACTIONr_mcbond_it1.0581.3971774
X-RAY DIFFRACTIONr_mcbond_other1.0571.3951773
X-RAY DIFFRACTIONr_mcangle_it1.7722.0912214
LS refinement shellResolution: 1.529→1.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 163 -
Rwork0.205 3054 -
all-3217 -
obs--67.03 %

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