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- PDB-4pnf: Glutathione S-Transferase from Drosophila melanogaster - isozyme E6 -

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Basic information

Entry
Database: PDB / ID: 4pnf
TitleGlutathione S-Transferase from Drosophila melanogaster - isozyme E6
ComponentsRE21095p
KeywordsTRANSFERASE / glutathione S-transferase / isozyme / glutathione complex
Function / homology
Function and homology information


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 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, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / 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 / RE21095p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsScian, M. / Le Trong, I. / Mannervik, B. / Atkins, W.M. / Stenkamp, R.E.
Funding support United States, Sweden, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF0051 United States
Swedish Research Council Sweden
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
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE21095p
B: RE21095p
C: RE21095p
D: RE21095p
E: RE21095p
F: RE21095p
G: RE21095p
H: RE21095p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,38116
Polymers205,9228
Non-polymers2,4598
Water13,133729
1
A: RE21095p
B: RE21095p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers51,4812
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area18380 Å2
MethodPISA
2
C: RE21095p
D: RE21095p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers51,4812
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-29 kcal/mol
Surface area18190 Å2
MethodPISA
3
E: RE21095p
F: RE21095p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers51,4812
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-28 kcal/mol
Surface area18650 Å2
MethodPISA
4
G: RE21095p
H: RE21095p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers51,4812
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-30 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.566, 208.494, 86.448
Angle α, β, γ (deg.)90.000, 92.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RE21095p


Mass: 25740.250 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstE6, CG17530
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7JZM3
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20% w/v PEG4000, 10% 2-propanol, 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: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.11→39.897 Å / Num. all: 102285 / Num. obs: 102285 / % possible obs: 96.2 % / Redundancy: 3.4 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Rsym value: 0.066 / Net I/av σ(I): 11.238 / Net I/σ(I): 16.2 / Num. measured all: 347743
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.11-2.222.90.3342.336497127630.2360.3343.382.7
2.22-2.363.50.2892.750752144540.1810.2894.998.5
2.36-2.523.50.1993.947094135920.1250.1996.698.5
2.52-2.723.50.1455.443778126120.0910.1458.998.3
2.72-2.983.50.17.941176116960.0620.112.599
2.98-3.343.40.06312.435998105440.040.06318.698.3
3.34-3.853.50.03819.83261893090.0240.03829.499
3.85-4.723.40.02727.62704778700.0170.02739.798.4
4.72-6.673.50.02826.32110960830.0180.02837.898.4
6.67-39.8973.50.01830.31167433620.0120.01853.198.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→39.897 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.482 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 5089 5 %RANDOM
Rwork0.1828 97133 --
obs0.1861 102222 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.8 Å2 / Biso mean: 34.655 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å21.36 Å2
2---3.04 Å20 Å2
3---1.43 Å2
Refinement stepCycle: final / Resolution: 2.11→39.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13985 0 160 729 14874
Biso mean--30.63 33.55 -
Num. residues----1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213822
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.97719692
X-RAY DIFFRACTIONr_angle_other_deg0.901331802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37951749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44124.313640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.951152368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0041562
X-RAY DIFFRACTIONr_chiral_restr0.1020.22238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023281
X-RAY DIFFRACTIONr_mcbond_it2.3653.3657020
X-RAY DIFFRACTIONr_mcbond_other2.3653.3647019
X-RAY DIFFRACTIONr_mcangle_it3.3555.0348761
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 263 -
Rwork0.239 5152 -
all-5415 -
obs--69.45 %

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