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- PDB-1v2a: Glutathione S-transferase 1-6 from Anopheles dirus species B -

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Basic information

Entry
Database: PDB / ID: 1v2a
TitleGlutathione S-transferase 1-6 from Anopheles dirus species B
Componentsglutathione transferase gst1-6
KeywordsTRANSFERASE / Glutathione S-Transferase / detoxification / glutathione / xenobiotics
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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 ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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
GLUTATHIONE SULFONIC ACID / glutathione transferase
Similarity search - Component
Biological speciesAnopheles dirus (mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOakley, A.J.
CitationJournal: Biochem.J. / Year: 2005
Title: Identification, characterization and structure of a new Delta class glutathione transferase isoenzyme.
Authors: Udomsinprasert, R. / Pongjaroenkit, S. / Wongsantichon, J. / Oakley, A.J. / Prapanthadara, L.A. / Wilce, M.C. / Ketterman, A.J.
History
DepositionOct 10, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2013Group: Other
Revision 1.4Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: glutathione transferase gst1-6
B: glutathione transferase gst1-6
C: glutathione transferase gst1-6
D: glutathione transferase gst1-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0658
Polymers96,6434
Non-polymers1,4214
Water3,747208
1
A: glutathione transferase gst1-6
B: glutathione transferase gst1-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0324
Polymers48,3222
Non-polymers7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-24 kcal/mol
Surface area18800 Å2
MethodPISA
2
C: glutathione transferase gst1-6
D: glutathione transferase gst1-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0324
Polymers48,3222
Non-polymers7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-24 kcal/mol
Surface area19380 Å2
MethodPISA
3
A: glutathione transferase gst1-6
B: glutathione transferase gst1-6
hetero molecules

C: glutathione transferase gst1-6
D: glutathione transferase gst1-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0658
Polymers96,6434
Non-polymers1,4214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area9600 Å2
ΔGint-64 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.203, 88.136, 200.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
glutathione transferase gst1-6 / glutathione S-transferase 1-6


Mass: 24160.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles dirus (mosquito) / Gene: AdGST1-6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BHB0, glutathione transferase
#2: Chemical
ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.16 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 22.5% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate/acetic acid pH 5.0, 10mM glutathione sulfonic acid, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.6-2 M1reservoirLi2SO4
21 mM1reservoirCuCl2
3100 mMsodium phosphate1reservoirpH6.5-7.5
413.1 mg/mlprotein1drop
510 mMglutathione sulphonic acid1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 25, 2001 / Details: Nickle Mirrors
RadiationMonochromator: Nickle mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 43837 / Num. obs: 43837 / % possible obs: 91.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.56
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2 / Num. unique all: 4242 / % possible all: 90.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JLV

1jlv


Resolution: 2.15→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2196 -RANDOM
Rwork0.234 ---
all-43382 --
obs-43382 91.5 %-
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2--8.78 Å20 Å2
3----10.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6735 0 92 208 7035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.381 349 -
Rwork0.311 --
obs-6904 88.8 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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