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- PDB-8udh: Crystal Structure of Mu class Glutathione-S-Transferase TuGSTm06(... -

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Basic information

Entry
Database: PDB / ID: 8udh
TitleCrystal Structure of Mu class Glutathione-S-Transferase TuGSTm06(Tetur05g05220) in complex with reaction product
ComponentsGlutathione-S-Transferase
KeywordsTRANSFERASE/PRODUCT / Glutathione-S-Transferase / Mu class GST TuGSTm06 / GST bound to BITC-SG / TRANSFERASE / TRANSFERASE-PRODUCT complex
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / 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
MALONATE ION / : / glutathione transferase
Similarity search - Component
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: Crystal Structure of Mu class Glutathione-S-Transferase TuGSTm06(Tetur05g05220) in complex with reaction product
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)54,59610
Polymers52,3622
Non-polymers2,2348
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-3 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.473, 133.473, 103.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
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: ILE / End label comp-ID: ILE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 224 / Label seq-ID: 2 - 224

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: 26180.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107360789 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1K569
#2: Chemical
ChemComp-WK6 / L-gamma-glutamyl-S-(benzylcarbamothioyl)-L-cysteinylglycine


Mass: 456.536 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.4 M sodium malonate

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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 EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 41596 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / CC1/2: 0.99 / CC star: 0.998 / Rpim(I) all: 0.398 / Rrim(I) all: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2003 / CC1/2: 0.733 / CC star: 0.92 / Rpim(I) all: 0.396 / Rrim(I) all: 0.607 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→34.603 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.566 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1927 2003 4.816 %
Rwork0.1719 39591 -
all0.173 --
obs-41594 96.184 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.952 Å2-0.476 Å20 Å2
2---0.952 Å20 Å2
3---3.088 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 148 301 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123879
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163552
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6475228
X-RAY DIFFRACTIONr_angle_other_deg0.7561.5628294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8135446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.5416.76534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48110682
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.40410180
X-RAY DIFFRACTIONr_chiral_restr0.0710.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024362
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02782
X-RAY DIFFRACTIONr_nbd_refined0.210.2803
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.23207
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21936
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2980.223
X-RAY DIFFRACTIONr_nbd_other0.2270.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0950.21
X-RAY DIFFRACTIONr_mcbond_it2.7193.0761787
X-RAY DIFFRACTIONr_mcbond_other2.7193.0761787
X-RAY DIFFRACTIONr_mcangle_it3.8424.5862232
X-RAY DIFFRACTIONr_mcangle_other3.8444.5912233
X-RAY DIFFRACTIONr_scbond_it4.4583.7362092
X-RAY DIFFRACTIONr_scbond_other4.4613.7382089
X-RAY DIFFRACTIONr_scangle_it6.4515.42996
X-RAY DIFFRACTIONr_scangle_other6.455.3992997
X-RAY DIFFRACTIONr_lrange_it8.60147.0544560
X-RAY DIFFRACTIONr_lrange_other8.57844.3674489
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.057236
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.104570.05007
12AX-RAY DIFFRACTIONLocal ncs0.104570.05007
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
2.05-2.1030.3111620.27429000.27631900.940.95195.98750.261
2.103-2.160.2551140.24129500.24231120.9640.96198.45760.222
2.16-2.2230.211330.21428610.21330570.9690.9797.93920.194
2.223-2.2910.2181220.20327170.20429100.970.97397.56010.18
2.291-2.3660.2161340.19426360.19628430.970.97797.43230.171
2.366-2.4480.2031140.18725030.18827190.9760.97996.24860.166
2.448-2.540.2051230.18224450.18326930.9740.9895.35830.161
2.54-2.6430.2251180.17322390.17625580.9690.98292.14230.154
2.643-2.760.2191180.18522710.18724220.9690.97998.63750.169
2.76-2.8940.2221070.17822190.1823620.9720.98198.47590.166
2.894-3.0490.1831070.17620870.17622410.980.98197.90270.169
3.049-3.2330.221210.19619350.19721140.9670.97997.25640.193
3.233-3.4540.185990.17518010.17519770.9780.98396.10520.177
3.454-3.7280.145860.1516150.14918550.9870.98791.69810.159
3.728-4.0790.172880.13914610.14116720.9820.98892.64350.154
4.079-4.5520.162620.12714540.12915570.9880.9997.36670.146
4.552-5.2410.157610.14512600.14513740.9860.98896.14260.171
5.241-6.3830.2690.189930.18111460.980.98392.67020.204
6.383-8.8770.24410.1837660.1869080.9780.98288.87670.214
8.877-34.6030.132230.1624770.165240.9880.98395.41980.217
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)
10.8604-0.3961-0.07132.6240.1271.6518-0.0844-0.103-0.10510.4320.07160.33670.03640.02160.01280.0730.01880.06050.05280.02480.0592-23.14-6.056-23.768
21.6682-0.56870.4031.04390.45881.648-0.05380.0267-0.4064-0.0479-0.02350.34190.1775-0.15940.07730.0608-0.0294-0.00640.1031-0.01870.1734-30.408-14.261-37.502
31.20020.02370.03511.95870.57861.7046-0.06030.05880.0564-0.221-0.0240.3349-0.1385-0.15970.08430.0435-0.0009-0.03510.04910.00960.0673-27.97210.999-38.532
42.48320.97151.36243.92670.66574.1332-0.1335-0.06510.4287-0.17750.04370.6217-0.4139-0.42430.08980.05090.0459-0.03150.07120.03520.1965-31.49622.845-36.714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 108
2X-RAY DIFFRACTION2ALLA109 - 224

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