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- PDB-9p6k: Colorado Potato Beetle Glutathione S-transferase Sigma Class member 2 -

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Basic information

Entry
Database: PDB / ID: 9p6k
TitleColorado Potato Beetle Glutathione S-transferase Sigma Class member 2
Componentsglutathione transferase
KeywordsTRANSFERASE / xenobiotic adaptation / detoxification / insecticide resistance / pesticide
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
glutathione transferase
Similarity search - Component
Biological speciesLeptinotarsa decemlineata (Colorado potato beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsMoural, T.W. / Zhu, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2144082 United States
United States Department of Agriculture (USDA)2020-67034-31780 United States
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Crystal structure and ligand binding of a sigma-class glutathione S-transferase associated with cross-resistance in a specialist herbivore.
Authors: Moural, T.W. / Hernandez, J.A. / Chen, Q.R. / Koirala Bk, S. / Liu, Y. / Cofer, T.M. / Zuo, I.X. / Alyokhin, A. / Wang, H. / Zhu, F.
History
DepositionJun 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione transferase
B: glutathione transferase
C: glutathione transferase
D: glutathione transferase


Theoretical massNumber of molelcules
Total (without water)103,2804
Polymers103,2804
Non-polymers00
Water00
1
A: glutathione transferase
B: glutathione transferase


Theoretical massNumber of molelcules
Total (without water)51,6402
Polymers51,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: glutathione transferase
D: glutathione transferase


Theoretical massNumber of molelcules
Total (without water)51,6402
Polymers51,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.372, 88.781, 97.902
Angle α, β, γ (deg.)90.000, 99.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 4 - 213 / Label seq-ID: 4 - 213

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.979305861115, -0.127253530717, 0.157373979124), (-0.14949277047, -0.0693366159266, -0.986328720696), (0.136425591303, -0.989443769303, 0.0488782715079)30.7328517969, 28.5457690307, 22.6243270666
2given(0.467208532983, 0.0327262911042, 0.883541270445), (-0.00615398900979, -0.9991701513, 0.0402633477364), (0.884125734908, -0.0242486828969, -0.466619423353)-20.4703457244, -11.4767730274, 26.8737906564
3given(-0.326146503776, -0.940848268546, 0.0918313326059), (0.151670402327, 0.0438040855964, 0.987460020023), (-0.933072637651, 0.335984728312, 0.12841228605)14.4565530269, -39.2929388325, 43.4468601466

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Components

#1: Protein
glutathione transferase


Mass: 25819.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptinotarsa decemlineata (Colorado potato beetle)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II / References: UniProt: A0A1P8PEX1, glutathione transferase
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.84→29.2 Å / Num. obs: 37601 / % possible obs: 97.28 % / Redundancy: 3.4 % / Biso Wilson estimate: 76.05 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08801 / Rpim(I) all: 0.05569 / Rrim(I) all: 0.1044 / Net I/av σ(I): 7.73 / Net I/σ(I): 7.73
Reflection shellResolution: 2.84→2.88 Å / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 722 / CC1/2: 0.408 / CC star: 0.777 / Rpim(I) all: 0.7198 / % possible all: 95.65

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→29.2 Å / SU ML: 0.5095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 3687 9.81 %
Rwork0.2205 33914 -
obs0.225 37601 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.08 Å2
Refinement stepCycle: LAST / Resolution: 2.84→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 0 0 6888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01367036
X-RAY DIFFRACTIONf_angle_d1.55799480
X-RAY DIFFRACTIONf_chiral_restr0.07551052
X-RAY DIFFRACTIONf_plane_restr0.01321192
X-RAY DIFFRACTIONf_dihedral_angle_d11.51832716
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.835777542565
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.880652322211
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.09553227604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.880.44851350.41711338X-RAY DIFFRACTION95.77
2.88-2.920.47111380.37731271X-RAY DIFFRACTION95.2
2.92-2.960.39621470.36011235X-RAY DIFFRACTION94.98
2.96-30.40721550.3481291X-RAY DIFFRACTION96.85
3-3.050.37781460.33781277X-RAY DIFFRACTION96.67
3.05-3.10.42621380.32011327X-RAY DIFFRACTION97.28
3.1-3.150.37421200.31561311X-RAY DIFFRACTION97.35
3.15-3.210.34521540.3081265X-RAY DIFFRACTION97.46
3.21-3.270.36211220.31431362X-RAY DIFFRACTION96.49
3.27-3.340.38661750.31471244X-RAY DIFFRACTION97.06
3.34-3.410.38111180.31191295X-RAY DIFFRACTION95.67
3.41-3.490.2681370.24591335X-RAY DIFFRACTION96.91
3.49-3.580.27431440.22111311X-RAY DIFFRACTION98.24
3.58-3.670.26731480.22931300X-RAY DIFFRACTION99.04
3.67-3.780.27371380.22821371X-RAY DIFFRACTION98.37
3.78-3.90.29781390.2031282X-RAY DIFFRACTION98.2
3.9-4.040.24811360.2011344X-RAY DIFFRACTION98.34
4.04-4.20.24531610.20161279X-RAY DIFFRACTION97.76
4.2-4.390.24781320.19081306X-RAY DIFFRACTION97.76
4.4-4.630.2091290.1681301X-RAY DIFFRACTION96.04
4.63-4.910.2421480.1771333X-RAY DIFFRACTION98.01
4.91-5.290.23171470.17551287X-RAY DIFFRACTION97.75
5.29-5.820.29591360.22231299X-RAY DIFFRACTION97.29
5.82-6.650.27811470.22511314X-RAY DIFFRACTION98.05
6.66-8.340.1871500.18951334X-RAY DIFFRACTION99.26
8.35-29.20.19321470.16441302X-RAY DIFFRACTION98.04
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.17395155825-0.194639819772-0.4851186470721.31575699652-0.1124025764684.674629311690.02454936141470.0838465215172-0.3145316506750.0393976401255-0.04651413615370.07664645063930.135971992616-0.230967047783-0.006014040329810.295853448940.0467464401586-0.2133183034130.406063700216-0.02272887582621.0036106744818.50549478793.451935168544.130387436
22.81221502781-0.105309863796-0.3823475915812.90071880387-0.4778913876134.13060350467-0.08674668252-0.148812020810.5913560184040.6627902842160.3485412961640.319493970374-0.750533977389-0.451940683805-0.1092472953570.5893705481530.190362418789-0.09746318375560.5331775641120.04329843583691.3354566202112.820882933421.46609527721.9353983209
34.35057332035-0.654306717147-0.1270955936236.535970615-0.8858551033783.84622451638-0.2443905702010.1000034392610.5513695413871.403224890050.5407513805580.637016268156-0.620838370093-0.538492855291-0.1869414307210.8449633681950.2225596809260.1201834359730.5820877854250.04685074361421.05171908761-8.06292809021-14.87411437141.2231658722
42.586612929720.4671099817610.03271450138954.59130943472-2.822885004775.27522809123-0.495924939011-0.0369906374358-0.507534728225-0.766799150058-0.00641215647637-1.264786914771.460868932140.04553179098060.3035287719730.876245239456-0.04688605010130.1136367009470.503879706571-0.002848813452621.491744907295.55341879724-32.257711791927.8687209475
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 4 - 213 / Label seq-ID: 1 - 210

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 4 through 213)AA
22(chain 'B' and resid 4 through 213)BB
33(chain 'C' and resid 4 through 213)CC
44(chain 'D' and resid 4 through 213)DD

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