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- PDB-1oyj: Crystal structure solution of Rice GST1 (OsGSTU1) in complex with... -

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Basic information

Entry
Database: PDB / ID: 1oyj
TitleCrystal structure solution of Rice GST1 (OsGSTU1) in complex with glutathione.
Componentsglutathione s-transferase
KeywordsTRANSFERASE / herbicide detoxification / plant glutathione S-transferase
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Probable glutathione S-transferase GSTU1 / Probable glutathione S-transferase GSTU1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDixon, D.P. / McEwen, A.G. / Lapthorn, A.J. / Edwards, R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Forced evolution of a herbicide detoxifying glutathione transferase.
Authors: Dixon, D.P. / McEwen, A.G. / Lapthorn, A.J. / Edwards, R.
History
DepositionApr 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Mar 21, 2012Group: Non-polymer description
Revision 1.5Apr 4, 2012Group: Non-polymer description
Revision 1.6Apr 25, 2012Group: Derived calculations
Revision 1.7Aug 16, 2023Group: 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 / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE At the time of processing, only a nucleotide sequence (GenBank accession AAAA01008376) was ...SEQUENCE At the time of processing, only a nucleotide sequence (GenBank accession AAAA01008376) was available. No corresponding protein sequence was available in a public sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione s-transferase
B: glutathione s-transferase
C: glutathione s-transferase
D: glutathione s-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,38443
Polymers103,6224
Non-polymers3,76239
Water11,007611
1
A: glutathione s-transferase
B: glutathione s-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,41220
Polymers51,8112
Non-polymers1,60118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-113 kcal/mol
Surface area19970 Å2
MethodPISA
2
C: glutathione s-transferase
D: glutathione s-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,97223
Polymers51,8112
Non-polymers2,16121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-99 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.829, 91.129, 165.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
glutathione s-transferase


Mass: 25905.553 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O65032, UniProt: Q10CE7*PLUS, glutathione transferase

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Non-polymers , 5 types, 650 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.74
Details: PEG 4000, magnesium chloride, HEPES, pH 7.74, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown / Details: Thom, R., (2002) Biochemistry, 41, 7008.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2002 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 85157 / Num. obs: 78138 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 1.95→2.001 Å

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GWC

1gwc


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.879 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22675 3635 5.1 %RANDOM
Rwork0.17786 ---
all0.1803 ---
obs0.1803 68290 84.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2--1.87 Å20 Å2
3----3.66 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 0 217 611 7911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0217482
X-RAY DIFFRACTIONr_bond_other_d0.0010.026856
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.98310097
X-RAY DIFFRACTIONr_angle_other_deg1.228315852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9913895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.757151261
X-RAY DIFFRACTIONr_chiral_restr0.2040.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028341
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021681
X-RAY DIFFRACTIONr_nbd_refined0.2660.31841
X-RAY DIFFRACTIONr_nbd_other0.2180.36573
X-RAY DIFFRACTIONr_nbtor_other0.1230.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.5592
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1840.517
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.333
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.375
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.562
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1160.51
X-RAY DIFFRACTIONr_mcbond_it1.2861.54471
X-RAY DIFFRACTIONr_mcangle_it2.13227104
X-RAY DIFFRACTIONr_scbond_it3.04633011
X-RAY DIFFRACTIONr_scangle_it4.7754.52993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.257 215
Rwork0.217 4019
obs-4019
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)
11.1569-0.0189-0.76640.86030.0871.83270.12010.15160.0641-0.054-0.01910.1056-0.2438-0.3116-0.1010.13920.04850.02310.07230.020.117929.18984.746233.2955
20.8635-0.0243-0.25990.6852-0.0742.2732-0.03090.0103-0.05060.0032-0.00580.01250.01780.23770.03680.1151-0.0062-0.00090.0401-0.00690.115343.9683-6.993140.5815
31.8351-1.0092-0.81461.57750.35822.2412-0.147-0.1591-0.14980.16330.07680.22680.2650.03590.07020.0730.00290.07610.06260.04480.152124.7587-6.484861.1306
41.1174-0.3257-0.17221.0777-0.62420.72850.1055-0.06920.20270.1003-0.0578-0.1419-0.2338-0.1009-0.04770.10710.00050.0780.02440.0040.174425.686313.612159.4548
51.3756-0.1792-0.45190.97720.02382.35160.14890.1160.0565-0.0412-0.06280.0635-0.2496-0.3223-0.08610.120.04520.010.10380.01630.095628.550650.547571.9272
60.6875-0.12250.39610.6775-0.09231.8159-0.01240.0671-0.0893-0.0062-0.033-0.03780.08230.16950.04540.1074-0.0032-0.01330.06190.0030.096543.626639.303579.3675
72.3581-0.9653-0.13421.29840.18382.4289-0.0945-0.2844-0.14320.04290.0990.13430.2072-0.0707-0.00440.0307-0.00260.04970.14620.04560.097424.839140.759899.8997
81.2347-0.3794-0.40191.24550.0422.19910.0757-0.1170.2316-0.00720.0174-0.2215-0.482-0.0679-0.09310.07380.01960.0580.0626-0.01740.132225.501860.871397.4962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 922 - 92
2X-RAY DIFFRACTION2AA95 - 23095 - 230
3X-RAY DIFFRACTION3BB3 - 923 - 92
4X-RAY DIFFRACTION4BB94 - 22794 - 227
5X-RAY DIFFRACTION5CC3 - 943 - 94
6X-RAY DIFFRACTION6CC95 - 22995 - 229
7X-RAY DIFFRACTION7DD4 - 924 - 92
8X-RAY DIFFRACTION8DD95 - 22795 - 227
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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