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- PDB-1jlv: Anopheles dirus species B glutathione S-transferases 1-3 -

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Basic information

Entry
Database: PDB / ID: 1jlv
TitleAnopheles dirus species B glutathione S-transferases 1-3
Componentsglutathione transferase GST1-3
KeywordsTRANSFERASE / glutathione S-transferase / GST / AdGST1-3
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / transferase activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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 domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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 / Glutathione transferase / Glutathione transferase GST1-3
Similarity search - Component
Biological speciesAnopheles cracens (mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOakley, A.J. / Harnnoi, T. / Udomsinprasert, R. / Jirajaroenrat, K. / Ketterman, A.J. / Wilce, M.C.
CitationJournal: Protein Sci. / Year: 2001
Title: The crystal structures of glutathione S-transferases isozymes 1-3 and 1-4 from Anopheles dirus species B.
Authors: Oakley, A.J. / Harnnoi, T. / Udomsinprasert, R. / Jirajaroenrat, K. / Ketterman, A.J. / Wilce, M.C.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione transferase GST1-3
B: glutathione transferase GST1-3
C: glutathione transferase GST1-3
D: glutathione transferase GST1-3
E: glutathione transferase GST1-3
F: glutathione transferase GST1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,70512
Polymers142,8616
Non-polymers1,8446
Water11,548641
1
A: glutathione transferase GST1-3
B: glutathione transferase GST1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2354
Polymers47,6202
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-33 kcal/mol
Surface area17290 Å2
MethodPISA
2
C: glutathione transferase GST1-3
D: glutathione transferase GST1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2354
Polymers47,6202
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-33 kcal/mol
Surface area17310 Å2
MethodPISA
3
E: glutathione transferase GST1-3
F: glutathione transferase GST1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2354
Polymers47,6202
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-33 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.810, 87.810, 166.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe asymmetric unit contains 3 copies of the biological assembly. These are composed of Chains A and B for the 1st assembly, chains C and D for the 2nd assembly, and chains E and F for the 3rd assembly.

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Components

#1: Protein
glutathione transferase GST1-3


Mass: 23810.162 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles cracens (mosquito) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GNE9, UniProt: Q7KIF2*PLUS, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG 4000, glutathione, dithiothreitol, acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium sulfate1reservoir
20.1 Msodium acetate1reservoirpH4.6
330 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5405 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 28, 2000 / Details: mirrors
RadiationMonochromator: Ni mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5405 Å / Relative weight: 1
ReflectionResolution: 1.75→15 Å / Num. all: 96781 / Num. obs: 96781 / % possible obs: 77 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.073 / Net I/σ(I): 9.4
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 10613 / Rsym value: 0.303 / % possible all: 85.1
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lucilia cuprina GST

Resolution: 1.75→17.22 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2857260.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4830 5 %RANDOM
Rwork0.223 ---
all0.223 97218 --
obs0.223 97218 77.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0286 Å2 / ksol: 0.385334 e/Å3
Displacement parametersBiso mean: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.75→17.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9954 0 120 641 10715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 878 4.8 %
Rwork0.281 17355 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GSH.PARGSH.TOP
Refinement
*PLUS
Num. reflection obs: 91965
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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