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- PDB-6tnl: GSTF1 from Alopecurus myosuroides -

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Basic information

Entry
Database: PDB / ID: 6tnl
TitleGSTF1 from Alopecurus myosuroides
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione-S-transferase / Ligandin / flavonoid binding / mult-herbicide resistence
Function / homology
Function and homology information


response to chemical / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 transferase
Similarity search - Component
Biological speciesAlopecurus myosuroides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsPohl, E. / Eno, R.F.M. / Freitag-Pohl, S. / Edwards, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/G006474/1 United Kingdom
CitationJournal: To Be Published
Title: GSTF1 from Alopecurus myosuroides
Authors: Pohl, E. / Eno, R.F.M. / Freitag-Pohl, S. / Edwards, R.
History
DepositionDec 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glutathione transferase
BBB: Glutathione transferase
CCC: Glutathione transferase
DDD: Glutathione transferase
EEE: Glutathione transferase
FFF: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2519
Polymers149,9636
Non-polymers2883
Water10,575587
1
AAA: Glutathione transferase

AAA: Glutathione transferase


Theoretical massNumber of molelcules
Total (without water)49,9882
Polymers49,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area2750 Å2
ΔGint-24 kcal/mol
Surface area16750 Å2
MethodPISA
2
FFF: Glutathione transferase
hetero molecules

BBB: Glutathione transferase


Theoretical massNumber of molelcules
Total (without water)50,0843
Polymers49,9882
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area2970 Å2
ΔGint-31 kcal/mol
Surface area16930 Å2
MethodPISA
3
CCC: Glutathione transferase
hetero molecules

CCC: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1804
Polymers49,9882
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
Buried area3050 Å2
ΔGint-43 kcal/mol
Surface area17060 Å2
MethodPISA
4
EEE: Glutathione transferase
hetero molecules

DDD: Glutathione transferase


Theoretical massNumber of molelcules
Total (without water)50,0843
Polymers49,9882
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
Buried area2930 Å2
ΔGint-30 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.780, 180.780, 237.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Glutathione transferase


Mass: 24993.783 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alopecurus myosuroides (plant) / Gene: GST2c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZS17, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate/PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 108121 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 5383 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→41.947 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.293 / WRfactor Rwork: 0.269 / Average fsc free: 0.9094 / Average fsc work: 0.9195 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2836 5353 4.991 %
Rwork0.2595 101894 -
all0.261 --
obs-107247 99.098 %
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: 35.856 Å2
Baniso -1Baniso -2Baniso -3
1-0.082 Å20.041 Å20 Å2
2--0.082 Å20 Å2
3----0.268 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9010 0 15 587 9612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0139309
X-RAY DIFFRACTIONr_bond_other_d0.0350.0178583
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.63612707
X-RAY DIFFRACTIONr_angle_other_deg2.3661.56719793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1351131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.6922.247454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.604151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8981543
X-RAY DIFFRACTIONr_chiral_restr0.0960.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0210339
X-RAY DIFFRACTIONr_gen_planes_other0.0230.022054
X-RAY DIFFRACTIONr_nbd_refined0.2360.21900
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.27136
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24581
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.23806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2439
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.258
X-RAY DIFFRACTIONr_nbd_other0.2230.2254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.233
X-RAY DIFFRACTIONr_mcbond_it1.7053.7264560
X-RAY DIFFRACTIONr_mcbond_other1.7043.7264559
X-RAY DIFFRACTIONr_mcangle_it2.8995.5595673
X-RAY DIFFRACTIONr_mcangle_other2.8995.565674
X-RAY DIFFRACTIONr_scbond_it2.1863.8974749
X-RAY DIFFRACTIONr_scbond_other2.153.894738
X-RAY DIFFRACTIONr_scangle_it3.5055.7677032
X-RAY DIFFRACTIONr_scangle_other3.4695.7577015
X-RAY DIFFRACTIONr_lrange_it5.52242.58310521
X-RAY DIFFRACTIONr_lrange_other5.50142.49110459
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
1.95-2.0010.3223710.32875370.32879200.8590.85799.84850.284
2.001-2.0550.3174100.31873210.31877430.8740.87999.8450.272
2.055-2.1150.3234030.30871320.30975590.8770.88499.68250.263
2.115-2.180.3323760.28969190.29173080.8760.999.82210.244
2.18-2.2510.3243260.29767110.29870500.8920.90499.81560.248
2.251-2.330.3013360.29364900.29468630.9070.91299.46090.244
2.33-2.4180.3143250.29762840.29866360.9010.91499.59310.248
2.418-2.5160.3153160.27760360.27963870.9040.92399.4520.236
2.516-2.6270.2612830.26458160.26361370.9310.93499.38080.228
2.627-2.7550.2782600.27355180.27358310.9270.93499.09110.246
2.755-2.9030.3062870.26452620.26756140.9330.93898.84220.242
2.903-3.0790.3212590.25949400.26252610.9070.94198.82150.248
3.079-3.290.3172440.26946720.27249910.9150.9498.49730.283
3.29-3.5520.2982510.25843290.2646680.9360.94898.11480.301
3.552-3.8880.2622110.23739470.23842590.9490.95597.62860.303
3.888-4.3420.2161870.21236000.21238900.9710.96797.35220.288
4.342-5.0050.2151810.21331840.21334510.9660.96697.5080.291
5.005-6.1080.2551410.2227710.22129420.9560.96598.98030.3
6.108-8.5480.2851270.21421680.21823140.9570.96799.17890.305
8.548-41.9470.296590.27912570.2813820.9410.95295.22430.449

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