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- PDB-1jlw: Anopheles dirus species B glutathione S-transferases 1-4 -

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Basic information

Entry
Database: PDB / ID: 1jlw
TitleAnopheles dirus species B glutathione S-transferases 1-4
Componentsglutathione transferase GST1-4
KeywordsTRANSFERASE / glutathione S-transferase / GST / AdGST1-4
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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
glutathione transferase / glutathione transferase
Similarity search - Component
Biological speciesAnopheles cracens (mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 GST1-4
B: glutathione transferase GST1-4


Theoretical massNumber of molelcules
Total (without water)50,0052
Polymers50,0052
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-17 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.440, 49.440, 271.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe asymetric unit represents the biological assembly, ie, a dimer of identical subunits

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Components

#1: Protein glutathione transferase GST1-4


Mass: 25002.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles cracens (mosquito) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GN60, UniProt: Q7KIF1*PLUS, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, glutathione, cacodylate, glycerol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Msodium acetate1reservoir
230 %PEG80001reservoir
30.1 Msodium cacodylate1reservoirpH6.5

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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: Apr 12, 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: 2.45→20 Å / Num. all: 14237 / Num. obs: 14237 / % possible obs: 93.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.8 Å2 / Rsym value: 0.077 / Net I/σ(I): 13.1
Reflection shellResolution: 2.45→2.54 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 1215 / Rsym value: 0.444 / % possible all: 83.7
Reflection
*PLUS

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Processing

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

Resolution: 2.45→19.92 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1983138.35 / 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
Rfree0.271 725 5.1 %RANDOM
Rwork0.223 ---
all0.223 14264 --
obs0.223 14264 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1135 Å2 / ksol: 0.373546 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å21.8 Å20 Å2
2--4.78 Å20 Å2
3----9.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 0 40 3532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 125 5.9 %
Rwork0.311 1996 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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