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- PDB-8udb: Crystal Structure of Mu class GST from TuGSTm12 (Tetur05g05300) f... -

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Basic information

Entry
Database: PDB / ID: 8udb
TitleCrystal Structure of Mu class GST from TuGSTm12 (Tetur05g05300) from Tetranychus urticae
ComponentsGlutathione-S-Transferase
KeywordsTRANSFERASE/SUBSTRATE / Glutathione-S-Transferase / GST bound to GSH / Mu class GST from Tetranychus urticae / 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
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKhatri, K. / Arriaza, R. / 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-Transferease (GST) from Tetranychus urticae
Authors: Khatri, K. / Ariazza, R. / 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)53,1674
Polymers52,5522
Non-polymers6152
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.464, 60.464, 234.998
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
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 - 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: 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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v polyethylene glycol 3,350
PH range: 7.5

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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: Aug 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 13765 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.046 / Rrim(I) all: 0.143 / Net I/σ(I): 18
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 661 / CC1/2: 0.73 / CC star: 0.919 / Rpim(I) all: 0.273 / Rrim(I) all: 0.782 / % 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: 2.75→39.197 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 31.245 / SU ML: 0.291 / Cross valid method: FREE R-VALUE / ESU R Free: 0.392
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2613 714 5.221 %
Rwork0.2149 12962 -
all0.217 --
obs-13676 99.687 %
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: 35.729 Å2
Baniso -1Baniso -2Baniso -3
1--1.514 Å2-0.757 Å2-0 Å2
2---1.514 Å20 Å2
3---4.911 Å2
Refinement stepCycle: LAST / Resolution: 2.75→39.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 40 64 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123733
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163382
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.6465049
X-RAY DIFFRACTIONr_angle_other_deg0.6591.5567884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3315446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.103521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85210640
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.52410174
X-RAY DIFFRACTIONr_chiral_restr0.0580.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024195
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02757
X-RAY DIFFRACTIONr_nbd_refined0.2070.2767
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.23059
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21835
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21756
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.28
X-RAY DIFFRACTIONr_nbd_other0.2810.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.22
X-RAY DIFFRACTIONr_mcbond_it0.9451.3431787
X-RAY DIFFRACTIONr_mcbond_other0.9451.3431787
X-RAY DIFFRACTIONr_mcangle_it1.6732.0082232
X-RAY DIFFRACTIONr_mcangle_other1.6732.0092233
X-RAY DIFFRACTIONr_scbond_it1.4291.5221946
X-RAY DIFFRACTIONr_scbond_other1.3961.521945
X-RAY DIFFRACTIONr_scangle_it2.0852.2292817
X-RAY DIFFRACTIONr_scangle_other2.0842.2332818
X-RAY DIFFRACTIONr_lrange_it5.21915.8114182
X-RAY DIFFRACTIONr_lrange_other5.2215.834182
X-RAY DIFFRACTIONr_ncsr_local_group_10.1240.056938
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.12360.05007
12AX-RAY DIFFRACTIONLocal ncs0.12360.05007
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
2.75-2.8210.332290.3149210.3159500.9520.941000.287
2.821-2.8980.338550.3149300.3159850.9140.941000.276
2.898-2.9810.429410.298730.2959140.9160.9471000.257
2.981-3.0730.371580.2678640.2739220.8940.9551000.237
3.073-3.1730.265340.2648610.2648960.9580.9599.88840.227
3.173-3.2830.286680.2587590.268270.9480.9521000.224
3.283-3.4060.318310.2518110.2538420.8980.9591000.225
3.406-3.5440.303480.2397580.2448060.9530.9631000.214
3.544-3.7010.238430.256860.2497570.9610.95996.30120.225
3.701-3.880.26300.2197110.2217430.9580.96699.73080.189
3.88-4.0870.234420.1786670.1817090.9620.9781000.158
4.087-4.3320.192400.1536430.1556840.9810.98699.85380.139
4.332-4.6270.246380.1655930.176320.9690.98299.84180.146
4.627-4.9920.212440.1485510.1535950.9740.9871000.134
4.992-5.460.25410.1865140.1915550.9750.981000.171
5.46-6.0890.301210.1984830.2025040.9680.9741000.181
6.089-7.0030.193160.2344360.2324520.9780.9661000.216
7.003-8.510.214150.1793820.183970.970.9791000.178
8.51-11.7610.207120.1723130.1743260.9780.98199.69330.187
11.761-39.1970.30680.2222060.2262150.9670.96999.53490.247
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)
10.83540.5175-0.07922.2497-0.56742.9424-0.03490.1276-0.1755-0.1388-0.1134-0.32820.05090.2840.14830.14990.05050.04060.24550.0260.112349.843-17.23920.603
21.9755-0.0783-0.34111.9441-0.55712.85050.09310.09420.1845-0.0433-0.069-0.0869-0.38690.0364-0.02410.28790.01830.03840.20840.04310.132746.367-1.88828.616
32.6153-1.3405-0.53332.37590.45711.91170.08350.1356-0.1977-0.13-0.19750.24960.0514-0.34850.1140.22710.00650.01660.2857-0.02620.132924.899-14.3924.22
43.2805-0.2552-0.44861.6719-0.54041.83880.10340.5733-0.1639-0.4106-0.2832-0.01490.0107-0.20030.17970.3340.0435-0.00250.337-0.11150.075328.838-17.5657.482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 109
2X-RAY DIFFRACTION2ALLA110 - 223

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