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- PDB-8uda: Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm12... -

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Basic information

Entry
Database: PDB / ID: 8uda
TitleCrystal Structure of Mu class Glutathione-S-Transferase, TuGSTm12(Tetur05g05300) from Tetranychus urticae
ComponentsGlutathione-S-Transferase
KeywordsTRANSFERASE/SUBSTRATE / Glutathione-S-Transferase / Mu class GST / Tetranychus urticae / TuGSTm12 / TRANSFERASE / TRANSFERASE-SUBSTRATE complex
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / identical protein binding
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
ACETATE ION / GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKhatri, K. / Arriaza, R.H. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)#2020-67014-31179 United States
CitationJournal: To Be Published
Title: Mu class GST from Tetranychus urticae
Authors: Khatri, K. / Arriaza, R.H. / Chruszcz, M.
History
DepositionSep 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 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-S-Transferase
B: Glutathione-S-Transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9775
Polymers52,5522
Non-polymers4253
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-19 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.086, 60.086, 472.821
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 223 / Label seq-ID: 2 - 223

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Glutathione-S-Transferase


Mass: 26275.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107360608 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1K577
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium malonate pH 6.0 and 12% w/v polyethylene glycol 3,350
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 13059 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.037 / Rrim(I) all: 0.117 / Net I/σ(I): 31.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 899 / CC1/2: 0.753 / CC star: 0.927 / Rpim(I) all: 0.256 / Rrim(I) all: 1.012 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.056 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: FREE R-VALUE / ESU R Free: 0.426
RfactorNum. reflection% reflection
Rfree0.2709 664 5.159 %
Rwork0.2111 12206 -
all0.214 --
obs-12870 93.928 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 107.875 Å2
Baniso -1Baniso -2Baniso -3
1-0.314 Å20.157 Å20 Å2
2--0.314 Å2-0 Å2
3----1.018 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 28 5 3561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123639
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.6474931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.87520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55910598
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.00910168
X-RAY DIFFRACTIONr_chiral_restr0.0840.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022772
X-RAY DIFFRACTIONr_nbd_refined0.2240.21689
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2114
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.23
X-RAY DIFFRACTIONr_mcbond_it5.8346.9481776
X-RAY DIFFRACTIONr_mcangle_it8.36210.4142214
X-RAY DIFFRACTIONr_scbond_it7.2727.1671863
X-RAY DIFFRACTIONr_scangle_it10.32210.6352717
X-RAY DIFFRACTIONr_lrange_it15.857133.38915452
X-RAY DIFFRACTIONr_ncsr_local_group_10.120.057001
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.120.05008
12AX-RAY DIFFRACTIONLocal ncs0.120.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.8-2.8720.329490.2659360.2689850.9370.9531000.245
2.872-2.9510.3440.2768720.2779160.9310.941000.255
2.951-3.0360.372430.2768880.2819310.8950.9421000.255
3.036-3.1280.31500.2628490.2658990.9340.9481000.233
3.128-3.230.411480.2848090.2918570.8580.9381000.254
3.23-3.3430.386460.278230.2778770.8520.94599.08780.246
3.343-3.4680.309450.2637450.2667980.9220.94898.99750.236
3.468-3.6090.3400.247260.2437910.9420.95796.83940.215
3.609-3.7680.291330.2466820.2497740.9350.95392.37730.226
3.768-3.950.245360.2136290.2157200.9470.96492.36110.198
3.95-4.1610.25380.1755630.187050.9530.97785.24820.163
4.161-4.410.239300.1875130.1896740.9570.97280.56380.181
4.41-4.710.254180.1844470.1876340.9620.97473.34380.193
4.71-5.0820.309250.1914530.1976010.9350.97479.53410.196
5.082-5.5570.347240.2274710.2335530.9070.96489.51170.231
5.557-6.1980.265280.2334620.2355180.9410.96494.59460.248
6.198-7.1260.214270.1924180.1944620.9730.97596.32040.197
7.126-8.6560.27150.1613920.1644230.9690.98496.21750.189
8.656-11.9520.129130.1453080.1443380.9960.98694.97040.171
11.952-39.0560.292120.2392160.2422320.980.96298.27590.299
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)
13.34520.3863-0.88993.9341-0.62263.225-0.0047-0.45850.04690.5416-0.0930.6485-0.2633-0.15210.09760.18460.0440.02860.19380.02930.4405-1.9333.219.102
24.0316-0.7228-0.50783.08550.03593.6794-0.0493-0.37220.22950.23260.1272-0.1856-0.51720.6433-0.0780.1902-0.0919-0.07080.17070.03090.485213.52738.70111.748
34.9749-0.6906-1.64721.435-0.4282.673-0.2151-0.6744-0.7627-0.1092-0.04520.20830.42920.49030.26030.20210.08230.08930.14660.13570.594814.41514.19615.335
45.1416-1.1625-0.72.211.3834.3736-0.5841-1.8949-1.38980.17180.28720.18910.5110.27890.29680.36540.20940.22990.71390.53960.66778.59612.58131.053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 107
2X-RAY DIFFRACTION2ALLA108 - 223

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