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- PDB-5f0g: Structure of the glutathione transferase delta 2 from Drosophila ... -

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Basic information

Entry
Database: PDB / ID: 5f0g
TitleStructure of the glutathione transferase delta 2 from Drosophila melanogaster
ComponentsGlutathione S-transferase D2
KeywordsTRANSFERASE / drosophila melanogaster / glutathion transferase / glutathion-S-transferase / GST / GST-D2 / GST delta 2
Function / homology
Function and homology information


glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
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 / 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 S-transferase D2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGonzalez, D. / Briand, L. / Neiers, F.
CitationJournal: Insect Biochem. Mol. Biol. / Year: 2018
Title: Characterization of a Drosophila glutathione transferase involved in isothiocyanate detoxification.
Authors: Gonzalez, D. / Fraichard, S. / Grassein, P. / Delarue, P. / Senet, P. / Nicolai, A. / Chavanne, E. / Mucher, E. / Artur, Y. / Ferveur, J.F. / Heydel, J.M. / Briand, L. / Neiers, F.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase D2
B: Glutathione S-transferase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1864
Polymers49,1242
Non-polymers622
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-33 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.500, 87.500, 53.200
Angle α, β, γ (deg.)90.00, 113.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase D2 / Glutathion transferase delta 2


Mass: 24562.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Synthetic gene / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstD2, GSTD2-2, gstD21, CG4181 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9VG98, glutathione transferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M succinic acid, phosphate, glycin (SPG buffer), 25% PEG 1500, pH = 4
PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→19.95 Å / Num. obs: 51278 / % possible obs: 97.6 % / Redundancy: 3.38 % / Rmerge(I) obs: 0.06004 / Net I/σ(I): 15.09
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.38 % / Mean I/σ(I) obs: 2.03 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EIN

3ein


Resolution: 1.6→19.95 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 2562 5 %
Rwork0.1716 --
obs0.1739 51225 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 2 517 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113396
X-RAY DIFFRACTIONf_angle_d1.2744611
X-RAY DIFFRACTIONf_dihedral_angle_d14.6541244
X-RAY DIFFRACTIONf_chiral_restr0.051493
X-RAY DIFFRACTIONf_plane_restr0.007592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63080.32421400.28472664X-RAY DIFFRACTION97
1.6308-1.6640.30571380.26732621X-RAY DIFFRACTION96
1.664-1.70020.27771420.25072700X-RAY DIFFRACTION98
1.7002-1.73970.27261410.23522676X-RAY DIFFRACTION98
1.7397-1.78320.27641420.23022708X-RAY DIFFRACTION97
1.7832-1.83140.26351430.22692701X-RAY DIFFRACTION97
1.8314-1.88520.26471400.21862670X-RAY DIFFRACTION98
1.8852-1.9460.25021410.20952674X-RAY DIFFRACTION98
1.946-2.01550.24721410.20122675X-RAY DIFFRACTION97
2.0155-2.09610.22791420.19272701X-RAY DIFFRACTION98
2.0961-2.19140.22111440.17622730X-RAY DIFFRACTION98
2.1914-2.30680.24531420.16632705X-RAY DIFFRACTION98
2.3068-2.45110.20131430.16492708X-RAY DIFFRACTION98
2.4511-2.640.22481430.16652731X-RAY DIFFRACTION98
2.64-2.90490.22451440.15982725X-RAY DIFFRACTION99
2.9049-3.32360.20441450.15712750X-RAY DIFFRACTION99
3.3236-4.1810.17321450.13952751X-RAY DIFFRACTION99
4.181-19.95340.18861460.14792773X-RAY DIFFRACTION98

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