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- PDB-7opz: Camel GSTM1-1 in complex with glutathione -

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Basic information

Entry
Database: PDB / ID: 7opz
TitleCamel GSTM1-1 in complex with glutathione
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / Detoxification / Pesticides / Adaptation
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / 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 / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPapageorgiou, A.C. / Poudel, N.
CitationJournal: Life / Year: 2022
Title: Structural and Functional Characterization of Camelus dromedarius Glutathione Transferase M1-1.
Authors: Perperopoulou, F. / Poudel, N. / Papageorgiou, A.C. / Ataya, F.S. / Labrou, N.E.
History
DepositionJun 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Glutathione transferase
A: Glutathione transferase
B: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4689
Polymers103,2164
Non-polymers1,2525
Water4,522251
1
C: Glutathione transferase
A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2455
Polymers51,6082
Non-polymers6383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-23 kcal/mol
Surface area19150 Å2
MethodPISA
2
B: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2224
Polymers51,6082
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-16 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.832, 150.151, 191.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Glutathione transferase


Mass: 25803.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: Cadr_000010866 / Production host: Escherichia coli (E. coli) / References: UniProt: G9B5E4, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.55 Å3/Da / Density % sol: 65.31 % / Description: Rod-like crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: Tris-HCl 100mM, PEG 4000 24% (w/v), sodium formate 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2017 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.55→95.9 Å / Num. obs: 49030 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.44 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.099 / Rrim(I) all: 0.188 / Net I/σ(I): 10.3
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 6.9 % / Num. unique obs: 4404 / CC1/2: 0.348 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTU
Resolution: 2.55→95.89 Å / SU ML: 0.3911 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 2393 4.89 %
Rwork0.2056 46522 -
obs0.2088 48915 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.1 Å2
Refinement stepCycle: LAST / Resolution: 2.55→95.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7232 0 81 251 7564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00797496
X-RAY DIFFRACTIONf_angle_d0.967710076
X-RAY DIFFRACTIONf_chiral_restr0.04781028
X-RAY DIFFRACTIONf_plane_restr0.00641288
X-RAY DIFFRACTIONf_dihedral_angle_d9.5621996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60.31151170.28422652X-RAY DIFFRACTION99.93
2.6-2.660.33271300.2882731X-RAY DIFFRACTION100
2.66-2.720.3541290.27912687X-RAY DIFFRACTION99.96
2.72-2.790.35031550.2712706X-RAY DIFFRACTION99.93
2.79-2.860.30061270.26372693X-RAY DIFFRACTION99.93
2.86-2.950.30171270.25452707X-RAY DIFFRACTION99.96
2.95-3.040.36391500.24632700X-RAY DIFFRACTION99.96
3.04-3.150.30011430.22942718X-RAY DIFFRACTION99.97
3.15-3.280.27491680.21742669X-RAY DIFFRACTION99.89
3.28-3.430.30551600.21082726X-RAY DIFFRACTION100
3.43-3.610.28541570.19342716X-RAY DIFFRACTION100
3.61-3.830.26291300.18092725X-RAY DIFFRACTION99.93
3.83-4.130.21741560.16062729X-RAY DIFFRACTION100
4.13-4.550.22591450.14722763X-RAY DIFFRACTION100
4.55-5.20.2241200.15662801X-RAY DIFFRACTION99.97
5.2-6.550.24111430.20262818X-RAY DIFFRACTION99.97
6.56-95.890.31441360.24962981X-RAY DIFFRACTION99.71
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.353335143010.9013764071830.9295810565881.504857378120.7884970537813.48866088926-0.09444796516250.245458216794-0.170472391698-0.2556793935890.266461293268-0.5046939197630.06165061052410.585906002674-0.1335255361180.380696450284-0.03028401870830.08606722684970.49956086848-0.0837443897320.532827614593-5.9988554653621.6245098053-35.2292024244
23.2404869258-0.729334866219-1.113157783221.127811485291.3234223371.58353288440.007445210012990.1195557375920.41628151267-0.233919333652-0.006291361484780.0528724845721-0.3064880915020.07309918293710.006059290704210.353179732168-0.0123837721256-0.0769445990850.362987613163-0.010104068430.307247550028-23.45319767926.9555572086-32.2273330239
32.81900025613-0.431714601637-0.2549911694614.42398230133-0.2365031624463.74116208341-0.277647874325-0.157545886538-0.2751722726960.1328635355210.3523644917170.5939829108750.438762823088-0.743412544975-0.04487190227350.382838326016-0.1122545792350.01116831736320.420859777293-0.07465745928110.375714128312-30.554426086414.2348663829-33.3931277484
41.06353616149-0.364508995655-0.1264665405433.691732195940.1489158204382.97522470715-0.0405471977310.0380244309108-0.0489745061277-0.815872545452-0.1336987723480.2999496597960.0459741699964-0.5647195389830.157035472320.367562099061-0.0264618366067-0.02372013042590.455846042308-0.07833633388260.372501486193-28.983401875115.9242177508-41.5157471215
53.71546824192-0.4108518786790.8662984345333.276879553110.4401732450626.125817002050.2060324030990.585602918407-0.398130445695-0.447018097328-0.674092172011-0.3508814254810.5258383560870.368158274070.3513687816870.484145583452-0.1205834869010.02884257009650.473869723988-0.03600432785310.482479085445-16.221880755718.2815178212-49.2959531066
66.46772278582-0.6128690561170.8305403161766.266178298170.241203243272.90008601638-0.147200471996-0.249059277704-0.519940682080.508219422669-0.220021946371-0.04721515951360.7421347432870.1937106402280.2251879730140.86960177866-0.0615291078519-0.139147697070.6309611794770.07023850890190.635914804565-13.22064868394.84581507971-34.1676275527
74.448495447450.6252211255920.9508682383411.542082525530.3772649686772.936771891530.0626412982977-0.534936367221-0.2139303188120.2870102513-0.03119288826510.1592911036190.348159498009-0.4618281656-0.0278418735970.3489276400090.006232267737350.05836674938490.4112959916060.0561166697890.359406929808-34.616405850624.2016209066-12.6200297467
84.283384370620.889000023233-0.4634176056994.0139401452-0.6567006148474.475075383490.09112650776490.1435820129720.2882781131290.05098939483840.02310329494280.275383824989-0.814591974924-0.239651543993-0.1220397356040.4004489865730.0756045485092-0.0166685644130.4360823146850.01801760913310.451579540759-29.770787614635.2244022698-21.9970906448
93.312950413032.19551203509-1.493781802533.06306129034-4.053313973877.05147019-0.354411171941-0.130844155549-0.374769290501-0.6122244757180.105541145715-0.7305600905890.540833083407-0.03755648977870.1964793527770.439572183923-0.0328181908657-0.01812844531660.393082876346-0.03853076925230.48537409909-15.327598273526.2642981396-20.3181138232
103.837501847990.5311612651310.6389990568023.646855826850.3219567301614.36176622609-0.188316151457-0.0990450259835-0.911853017469-0.05928999910650.149442152837-0.794446276380.959583369260.5254475440220.01485860180650.5379140266650.0902727037104-0.05041982441750.5351239615790.0576294938430.529282665661-7.6875152693518.1636494632-11.5844502588
113.77475413443-0.213174112495-4.72989863898.298655508651.153454781736.036811587210.1899617061960.5183732384720.6550240624380.0414881701553-0.5597377218240.70976442371-0.564589081416-0.7441258985010.3739733910.438932460551-0.0350206960306-0.1027001617870.353848122287-0.09214664943710.475652339019-11.064147717341.1238768591-16.5054649579
122.011675888920.372281236517-0.8187161417283.54325873815-0.7164460619912.94745760156-0.0162446127876-0.3536216311670.05543030175940.475477038718-0.108226571903-0.318599748825-0.04315289631330.5930071606380.1039090481250.3584221912990.0150934388679-0.02656228309880.426889168642-0.05903944888390.368784296983-11.64670263430.8568886695-7.95065530201
131.48803620847-0.177022472118-0.5661349260811.069851907440.2205776632552.415673109310.148440973444-0.1806931334890.03683927320870.2228208126010.02159301323250.0706282501412-0.3411170322260.6032618233230.03476581721980.675848716107-0.0328617272081-0.0272396475710.771948532565-0.1453197227640.676418922498-24.873378027734.2520988673-2.26721943947
147.69775922424-0.8886933744831.74896026583.0318227324-0.5837841909462.778436823270.362782911165-0.905281118171-0.3717093244030.443383876725-0.568280758615-0.1583589701111.497135235770.3413796748610.03519006734540.810273318812-0.004539578978420.0002161529153660.7712516543260.1549487865570.702742913023-23.555905480314.3454436759-4.83933129113
154.99863777749-1.409143301410.07818148447543.138254504720.1161738556012.49646155809-0.177309800306-0.3328828883030.08597397572570.9086773821410.080351493082-0.4901972206620.572787817990.2073955272450.0923047114990.7541962088420.0547754365023-0.07771241376940.53859350406-0.04250527829830.482002760411-12.1385113471-7.80821900214-47.1222423787
161.17061801011-0.954008060980.5055646412194.247018274550.2933694149881.92312539280.08097737219440.05843618284670.8226122535541.198553526490.191216342014-1.26481589954-0.473270544380.856891640756-0.07862763444580.772988363362-0.16746956381-0.1039068298460.767707356033-0.1145860127730.9867620514443.609551796582.59534350534-51.6526793318
172.80792139775-0.6033190307710.8871055103222.187774643260.1384819318442.52769691007-0.1061956167490.259178682198-0.5564628793830.9535968578670.413122160481-0.5361891610220.3105587024020.626898168843-0.2904244807350.6893154216890.124279606418-0.1787507185390.559736327532-0.1219796252340.643850023001-2.85870615402-14.1468581373-54.5129229306
181.89020565865-0.7243132239330.5567124100521.938654283871.585725838394.36522054351-0.1096239677630.158349782395-0.216237799685-0.0931424933370.03103966623350.05919972751950.482336745159-0.01362937186440.06607988853760.538163126836-0.0955069563580.0578653907460.456301894983-0.1181263879650.467108044582-20.5369356796-8.84634494821-61.1262887767
193.068557376911.750276739310.6047390802274.070601280230.887754433683.65357028917-0.1210053985220.5200109671930.276257500737-0.463413525160.08281331805050.237332524346-0.7711005322330.07488622862510.08033638336160.7096476257020.07714122520160.01619602104720.565717694579-0.03493165153180.517177612077-21.659062136310.3913062408-65.1421861787
200.77835920026-1.08306915447-0.1552511404481.61551088504-0.3355930469782.144681326610.127086745127-0.163770730871-0.1308403913660.107205112966-0.2937520423030.486757308190.201432552134-0.2503978498450.1884011925710.615579482058-0.1629946799810.06512936374160.543426858099-0.1068401278060.558701527959-27.2954684137-3.06042029919-56.2760835514
214.47647053993-0.6027920944961.014112474115.21877806898-0.9085036597186.529282037190.002567214890220.5191423384170.21226697798-0.1271092928250.06937925577590.2739490364450.0601850072999-1.38245943511-0.2372365946910.496040873451-0.04624962007520.06413851803620.66503651348-0.1448037159710.498647318833-31.27805806935.2962298929-54.4337360296
222.770967093211.54191674265-2.235675786222.28009008651-0.1440951542213.599731357630.186875845490.505107813918-0.4246757956841.060880779510.162355566852-0.312446623217-0.663563884201-0.458045787363-0.3256191877240.7522651924560.06265855660550.03874196599180.536430234201-0.01798452219880.499146129472-20.4297192815-1.73571001501-42.2330221534
232.641459924151.200611987960.008698378454614.88555541288-0.2755195772144.625810008290.1952492629824.29873922164E-5-0.136890570040.613389726033-0.5934737340570.0120683451396-1.045704528250.2794115913070.6019970534380.696279527406-0.1379527943410.01745000290280.685181807266-0.085875807210.712143825922-7.859173135979.98984874503-53.8372734615
243.35788679844-3.13934973271-1.049961287995.15897284243-1.506835627752.966066983710.142113433050.662802939579-0.0660482782056-0.562195022309-0.2519730514110.274421928896-0.284392876560.02697414022480.1323116724230.541576992266-0.0648062103384-0.001797575064390.480379619559-0.1203496888630.412571883637-19.7019662954-12.1478343374-84.3658349691
256.655634949932.04313112251-1.873091445444.98631084276-3.91011787164.74116218022-0.3087835540320.2627221520111.51221502394-1.098403970470.57747481584-0.96708222771-0.9353681052750.501744376614-0.4197491505281.52175718318-0.08500902637460.3163925398620.954642639771-0.03171765390581.2521442458-15.41334617818.52756828138-87.2124071021
262.61541300985-1.586059221380.7167475748223.162101861210.980801075924.38880631359-0.1122476685750.0825603168157-0.08637707374420.1024917469180.09774565744830.1225499710290.00542049636422-0.3607864978090.04271674527480.437879608557-0.0653782426340.05473559440470.452191925255-0.0841223275380.368620759484-19.310512068-10.6202999316-72.9054789358
273.232521932071.253697183960.4024230630364.663826844380.2124808603282.66133237325-0.104235290560.1138733918210.231535406542-0.5215360176150.246512053244-1.06459236103-0.5857396653990.895619568267-0.1640855951120.709929460545-0.1325928679880.1359982233320.837218687223-0.2272270069990.7722083222643.47426889119-5.39915451488-72.6009470094
282.49389307754-0.1258195179540.5952181960712.97632923725-0.5096814414873.75414286547-0.01845044619670.0452292131633-0.162085745657-0.1339606693680.298938047599-0.9681245415860.2213024780060.7223226355-0.2225240590770.4439630264990.02101015640730.0529333112960.55307350506-0.1961705384570.62568933231-2.47129244627-19.6354177137-76.120019156
294.901290619190.788453756930.04120222637966.53470067364-3.31910041927.075584848140.0368649038270.717369080094-0.0834017621171-0.0187423358716-0.0791774585483-0.3036756744230.604214738695-0.08161500564670.1920452249430.6144296852640.07255280728480.06938283074310.539995845381-0.1383053852880.47761711223-11.0731847642-23.4211274247-88.1066231426
305.505599379182.832876788981.045068825546.902287376161.693536826814.982801880980.941059426981-0.5526608836551.372663588691.01740014664-1.453902783450.0284831495855-0.1755002938650.263128612320.3017049992690.782253400157-0.1341309625550.08409386619240.842216621617-0.05810093918190.772639365272-8.04547938356-4.43686947628-87.2564058079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 71 )
2X-RAY DIFFRACTION2chain 'C' and (resid 72 through 114 )
3X-RAY DIFFRACTION3chain 'C' and (resid 115 through 153 )
4X-RAY DIFFRACTION4chain 'C' and (resid 154 through 189 )
5X-RAY DIFFRACTION5chain 'C' and (resid 190 through 207 )
6X-RAY DIFFRACTION6chain 'C' and (resid 208 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 60 )
8X-RAY DIFFRACTION8chain 'A' and (resid 61 through 89 )
9X-RAY DIFFRACTION9chain 'A' and (resid 90 through 115 )
10X-RAY DIFFRACTION10chain 'A' and (resid 116 through 141 )
11X-RAY DIFFRACTION11chain 'A' and (resid 142 through 153 )
12X-RAY DIFFRACTION12chain 'A' and (resid 154 through 189 )
13X-RAY DIFFRACTION13chain 'A' and (resid 190 through 207 )
14X-RAY DIFFRACTION14chain 'A' and (resid 208 through 217 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1 through 32 )
16X-RAY DIFFRACTION16chain 'B' and (resid 33 through 46 )
17X-RAY DIFFRACTION17chain 'B' and (resid 47 through 71 )
18X-RAY DIFFRACTION18chain 'B' and (resid 72 through 115 )
19X-RAY DIFFRACTION19chain 'B' and (resid 116 through 141 )
20X-RAY DIFFRACTION20chain 'B' and (resid 142 through 169 )
21X-RAY DIFFRACTION21chain 'B' and (resid 170 through 188 )
22X-RAY DIFFRACTION22chain 'B' and (resid 189 through 207 )
23X-RAY DIFFRACTION23chain 'B' and (resid 208 through 217 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 32 )
25X-RAY DIFFRACTION25chain 'D' and (resid 33 through 42 )
26X-RAY DIFFRACTION26chain 'D' and (resid 43 through 114 )
27X-RAY DIFFRACTION27chain 'D' and (resid 115 through 141 )
28X-RAY DIFFRACTION28chain 'D' and (resid 142 through 188 )
29X-RAY DIFFRACTION29chain 'D' and (resid 189 through 198 )
30X-RAY DIFFRACTION30chain 'D' and (resid 199 through 217 )

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