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- PDB-7opy: Camel GSTM1-1 in complex with S-(p-nitrobenzyl)glutathione -

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Basic information

Entry
Database: PDB / ID: 7opy
TitleCamel GSTM1-1 in complex with S-(p-nitrobenzyl)glutathione
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / Detoxification / Pesticides / Adaptation
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / lipid metabolic process / identical protein binding / cytoplasm
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
FORMIC ACID / S-(P-NITROBENZYL)GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,12313
Polymers103,2164
Non-polymers1,9089
Water7,260403
1
F: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6088
Polymers51,6082
Non-polymers1,0006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-44 kcal/mol
Surface area19260 Å2
MethodPISA
2
A: Glutathione transferase
C: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5165
Polymers51,6082
Non-polymers9083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-29 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.388, 177.376, 59.420
Angle α, β, γ (deg.)90.000, 115.002, 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

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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-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H22N4O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.25 % / Description: Rod-like crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: Tris-HCl 100 mM, PEG 4000 24% (w/v), sodium formate 0.2 M, 2.5 mM GTB

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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: 2.05→88.7 Å / Num. obs: 55058 / % possible obs: 93.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.984 / Rpim(I) all: 0.106 / Rrim(I) all: 0.175 / Net I/σ(I): 5
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 2.8 % / Num. unique obs: 4146 / CC1/2: 0.305 / % possible all: 90.5

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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

1gtu


Resolution: 2.05→88.69 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 2627 4.79 %
Rwork0.1926 52247 -
obs0.1954 54874 93.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.61 Å2
Refinement stepCycle: LAST / Resolution: 2.05→88.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7232 0 127 403 7762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00797542
X-RAY DIFFRACTIONf_angle_d0.942610137
X-RAY DIFFRACTIONf_chiral_restr0.04711028
X-RAY DIFFRACTIONf_plane_restr0.0051296
X-RAY DIFFRACTIONf_dihedral_angle_d12.29171004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.37221260.31172611X-RAY DIFFRACTION89.62
2.09-2.130.34281330.27982652X-RAY DIFFRACTION89.26
2.13-2.170.3481420.2532655X-RAY DIFFRACTION90.55
2.17-2.220.30591290.22812772X-RAY DIFFRACTION92.8
2.22-2.270.29911440.24562758X-RAY DIFFRACTION93.95
2.27-2.330.30751580.22882753X-RAY DIFFRACTION94.7
2.33-2.390.2831570.22812811X-RAY DIFFRACTION94.55
2.39-2.460.29471220.20872798X-RAY DIFFRACTION94.84
2.46-2.540.24571360.2022759X-RAY DIFFRACTION93.78
2.54-2.630.28211230.19632806X-RAY DIFFRACTION93.67
2.63-2.740.26691370.21772788X-RAY DIFFRACTION94.94
2.74-2.860.29741210.21422814X-RAY DIFFRACTION95.11
2.86-3.010.29111700.20792786X-RAY DIFFRACTION94.53
3.01-3.20.28621590.2072713X-RAY DIFFRACTION92.91
3.2-3.450.24991430.18942767X-RAY DIFFRACTION93.51
3.45-3.790.21791310.16682771X-RAY DIFFRACTION93.82
3.79-4.340.20841300.14882768X-RAY DIFFRACTION93.09
4.34-5.470.19691380.15762758X-RAY DIFFRACTION91.91
5.47-88.690.22671280.19042707X-RAY DIFFRACTION90.43
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)
16.580329811451.237205588331.028637249772.308710963381.142534107181.745763469390.427389780967-1.06665840236-0.2302785209940.638071830955-0.237410701064-0.2196841494150.397705422798-0.156752494384-0.1172405670130.43385752262-0.0556075009206-0.08485974318240.3353464522170.007889446688860.196381219224-1.139659004170.95705345631816.1542162134
25.37599788359-1.017981554890.4667455760513.451621147380.7277947405012.91915299018-0.245312985644-1.175903239650.1005644503440.5012407214520.323131683706-0.0981439296067-0.00997525435422-0.147743648034-0.06592071197280.2752863460950.05766712408470.0290818733380.384772602965-0.09817583715530.244019030305-29.2710569952-37.216960561737.6855758873
35.952638164470.6225522046510.3694643222152.410815853550.194556209944.394461762520.09611442308081.663796230950.117368149429-0.4579983765270.1121903894430.0643804685992-0.06128778517290.0495134589449-0.02616811732770.3206137333090.0743728577109-0.04549673104030.545001919863-0.1102785746950.215865515884-4.08735067961.76810102886-9.14578329892
46.50713916841-1.31929776052-1.06337066732.64296770860.8131993435113.646789953240.3799618296711.80416068815-0.301994429303-0.980968685598-0.219101918575-0.387758143725-0.28210155009-0.334099192112-0.0941825586720.4794382884430.01660193950480.135733334360.671327696993-0.1462661383490.35610491122-26.2643051298-37.653488823112.4734156859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'F' and resid 1 through 217)
2X-RAY DIFFRACTION2(chain 'A' and resid 1 through 217)
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 217)
4X-RAY DIFFRACTION4(chain 'C' and resid 1 through 217)

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