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- PDB-6riv: Crystal structure of Alopecurus myosuroides GSTF -

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Basic information

Entry
Database: PDB / ID: 6riv
TitleCrystal structure of Alopecurus myosuroides GSTF
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / detoxification / xenobiotics
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
S-Hydroxy-Glutathione / SUCCINIC ACID / glutathione transferase
Similarity search - Component
Biological speciesAlopecurus myosuroides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsPapageorgiou, A.C. / Poudel, N.
CitationJournal: Plant Physiol Biochem. / Year: 2020
Title: Comparative structural and functional analysis of phi class glutathione transferases involved in multiple-herbicide resistance of grass weeds and crops.
Authors: Georgakis, N. / Poudel, N. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,09913
Polymers51,9862
Non-polymers1,11311
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-64 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.289, 50.708, 51.603
Angle α, β, γ (deg.)97.740, 110.240, 110.960
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Glutathione transferase


Mass: 25992.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cys122 was found oxidised and modelled as CSO / Source: (gene. exp.) Alopecurus myosuroides (plant) / Gene: GST2c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZS17, glutathione transferase

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Non-polymers , 5 types, 449 molecules

#2: Chemical ChemComp-GS8 / S-Hydroxy-Glutathione


Mass: 323.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O7S
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M SPG, pH 5; 25% w/v PEG 1500

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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 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.33→46.2 Å / Num. obs: 93011 / % possible obs: 94.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Net I/σ(I): 17
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1536 / CC1/2: 0.7 / Rrim(I) all: 0.693 / % possible all: 32

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AW9

1aw9


Resolution: 1.33→46.2 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.707 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 4463 4.8 %RANDOM
Rwork0.1309 ---
obs0.1325 88547 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.67 Å2 / Biso mean: 21.201 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20.23 Å20.19 Å2
2---0.53 Å20.35 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.33→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 70 438 3994
Biso mean--25.07 33.54 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193663
X-RAY DIFFRACTIONr_bond_other_d0.0030.023375
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.974982
X-RAY DIFFRACTIONr_angle_other_deg1.0973.0037839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17123.827162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60215591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1321518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02748
X-RAY DIFFRACTIONr_rigid_bond_restr3.29337038
X-RAY DIFFRACTIONr_sphericity_free24.7085287
X-RAY DIFFRACTIONr_sphericity_bonded9.69457096
LS refinement shellResolution: 1.33→1.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 161 -
Rwork0.236 3170 -
all-3331 -
obs--45.82 %

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