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- PDB-1bye: GLUTATHIONE S-TRANSFERASE I FROM MAIS IN COMPLEX WITH ATRAZINE GL... -

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Basic information

Entry
Database: PDB / ID: 1bye
TitleGLUTATHIONE S-TRANSFERASE I FROM MAIS IN COMPLEX WITH ATRAZINE GLUTATHIONE CONJUGATE
ComponentsPROTEIN (GLUTATHIONE S-TRANSFERASE)
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / HERBICIDE
Function / homology
Function and homology information


response to salicylic acid / glutathione binding / response to herbicide / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to reactive oxygen species / response to hydrogen peroxide / response to xenobiotic stimulus / protein-containing complex / cytoplasm
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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATRAZINE GLUTATHIONE CONJUGATE / Glutathione S-transferase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPrade, L. / Huber, R. / Bieseler, B.
CitationJournal: Structure / Year: 1998
Title: Structures of herbicides in complex with their detoxifying enzyme glutathione S-transferase - explanations for the selectivity of the enzyme in plants.
Authors: Prade, L. / Huber, R. / Bieseler, B.
History
DepositionOct 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8088
Polymers94,8614
Non-polymers1,9464
Water86548
1
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4044
Polymers47,4312
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-23 kcal/mol
Surface area17440 Å2
MethodPISA
2
C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4044
Polymers47,4312
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-23 kcal/mol
Surface area17530 Å2
MethodPISA
3
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules

A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules

C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules

C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,61516
Polymers189,7238
Non-polymers3,8928
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_444x-1/2,y-1/2,z-11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area27560 Å2
ΔGint-137 kcal/mol
Surface area60940 Å2
MethodPISA
4
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules

C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8088
Polymers94,8614
Non-polymers1,9464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area12810 Å2
ΔGint-62 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.610, 60.280, 121.430
Angle α, β, γ (deg.)90.00, 126.22, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.530034, 0.441304, 0.724096), (-0.104256, 0.881346, -0.460825), (-0.841543, 0.168762, 0.513152)
Vector: -56.9621, -1.6398, -36.4235)

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Components

#1: Protein
PROTEIN (GLUTATHIONE S-TRANSFERASE)


Mass: 23715.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P12653
#2: Chemical
ChemComp-ATA / ATRAZINE GLUTATHIONE CONJUGATE


Mass: 486.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H30N8O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
25 mMatrazine-GSH conjugate1drop
30.1 MMES1reservoir
420-25 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→12 Å / Num. obs: 22535 / % possible obs: 89.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Redundancy: 2 %
Reflection shell
*PLUS
% possible obs: 84.9 % / Rmerge(I) obs: 0.483

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXD

1axd


Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.305 -5 %RANDOM
Rwork0.221 ---
obs-22535 89.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6664 0 132 48 6844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d3.61
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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