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- PDB-6zb6: Crystal structure of Lolium rigidum GSTF in complex with S-(p-nit... -

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Basic information

Entry
Database: PDB / ID: 6zb6
TitleCrystal structure of Lolium rigidum GSTF in complex with S-(p-nitrobenzyl) glutathione
ComponentsGlutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / GLUTATHIONE / DETOXIFICATION / XENOBIOTICS / HERBCIDE RESISTANCE / STRESS
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / 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 / S-(P-NITROBENZYL)GLUTATHIONE / Glutathione transferase
Similarity search - Component
Biological speciesLolium rigidum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPapageorgiou, A.C. / Poudel, N.
Funding support Greece, 1items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)8904/22-09-2017 Greece
CitationJournal: Plant Physiol Biochem. / Year: 2021
Title: Phi class glutathione transferases as molecular targets towards multiple-herbicide resistance: Inhibition analysis and pharmacophore design.
Authors: Georgakis, N. / Poudel, N. / Vlachakis, D. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionJun 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,26931
Polymers155,6226
Non-polymers3,64725
Water19,3301073
1
A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6337
Polymers25,9371
Non-polymers6966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4944
Polymers25,9371
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4713
Polymers25,9371
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7948
Polymers25,9371
Non-polymers8577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5175
Polymers25,9371
Non-polymers5814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3594
Polymers25,9371
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.562, 98.500, 95.900
Angle α, β, γ (deg.)90.000, 109.126, 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

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Protein , 1 types, 6 molecules ACEBFD

#1: Protein
Glutathione transferase / Glutathione S-transferase


Mass: 25936.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lolium rigidum (plant) / Gene: GST / Production host: Escherichia coli (E. coli) / References: UniProt: M5BPX4

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Non-polymers , 5 types, 1098 molecules

#2: Chemical
ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H22N4O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 1073 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.66 % / Description: Thin rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% w/v Sokalan PA 25CL, 0.1 M Hepes, 0.1 M Sodium tartrate

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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: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→66.7 Å / Num. obs: 126047 / % possible obs: 98.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.15 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.113 / Net I/σ(I): 7.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5801 / CC1/2: 0.843 / Rpim(I) all: 0.583 / Rrim(I) all: 0.862 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bye

1bye


Resolution: 1.9→66.68 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2029 1829 1.45 %
Rwork0.1643 123982 -
obs0.1649 125811 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→66.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 239 1073 11820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006711026
X-RAY DIFFRACTIONf_angle_d0.832114932
X-RAY DIFFRACTIONf_chiral_restr0.05171601
X-RAY DIFFRACTIONf_plane_restr0.00621906
X-RAY DIFFRACTIONf_dihedral_angle_d7.08661471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31141340.28378946X-RAY DIFFRACTION92.72
1.95-2.010.35771400.2369558X-RAY DIFFRACTION98.74
2.01-2.070.2571460.21519517X-RAY DIFFRACTION98.4
2.07-2.150.26051440.19639562X-RAY DIFFRACTION98.87
2.15-2.230.2221300.18789543X-RAY DIFFRACTION98.68
2.23-2.340.21831400.17649509X-RAY DIFFRACTION98.27
2.34-2.460.18111400.1639608X-RAY DIFFRACTION99.4
2.46-2.610.20291420.16749570X-RAY DIFFRACTION99.17
2.61-2.810.23631490.16729594X-RAY DIFFRACTION98.61
2.81-3.10.19431410.16839534X-RAY DIFFRACTION98.47
3.1-3.550.18341370.15849618X-RAY DIFFRACTION98.76
3.55-4.470.16951440.13049688X-RAY DIFFRACTION99.44
4.47-66.680.17831420.14549735X-RAY DIFFRACTION98.47
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)
10.838884587132-0.333076892302-0.4229079421480.679318266330.2144380293540.8160643163750.0265525125690.0505986433480.0100120262293-0.103736215648-0.0220575678438-0.0529344122523-0.07901208988330.09221632575645.34708304986E-60.161677601603-0.00849059846352-0.003522064620750.15475391719-0.01236775545910.168163853183-14.5765106983-22.0772942223129.481616517
20.97745125544-0.0775162176987-0.5132475694020.4370133819470.04987013655331.190686339790.06877204946580.117130669757-0.02186388461030.00894675824537-0.05362637675510.100345122103-0.0918634531712-0.2868277711470.0007768429807740.1645464453070.003239067898950.009981902476860.174700132382-0.009893535474180.165342629193-3.8097733351314.432584475971.6936755744
30.998150936042-0.207222563174-0.04840862788180.5845956286820.09665187500050.580112863650.0186079075312-1.57987651761E-5-0.05625442447040.113238581406-0.05441774775580.05239477678290.0670691414008-0.101817512064-0.0003873358658560.1803701985240.02141640735620.01250645559520.1819289324530.001002538594720.172605409159-34.23188441989.81520376303116.456846275
41.2351723320.118906500236-0.5200727394470.575143926223-0.1859841560441.198598235370.006682546991750.216704710227-0.0637722564735-0.0258124781558-0.03048851100930.05156421630140.0409666064994-0.2446514001490.0007393742678170.1593874927830.0259242289536-0.0009405236140160.167454820563-0.0133440396090.16863794303910.5709154063-37.6290350256104.71606992
50.8636047687540.0880201765195-0.4186885253110.838301302154-0.2906036589921.18112232285-0.0405026356625-0.235321563251-0.221648272770.0297385611478-0.08658478507130.01139539558990.09423321911490.043628053997-0.06139119318220.140869895503-0.01541545291990.006482295033830.1713694386550.05165393538020.199743016307-21.3912888363-35.675302469148.094358238
61.004886515620.129774998526-0.3665216310380.635483350552-0.09252651079641.011417485880.1558521780670.1714240207230.229133395265-0.02631431656970.0118645427157-0.0116123309182-0.252942001598-0.09514208198050.1699261808980.2107180867180.06309347573820.04756340446630.1756975848420.03501988364220.174916119589-25.51856004227.2982058937101.719274015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 222)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 215)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 227)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 215)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 215)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 215)

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