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- PDB-5ft3: Aedes aegypti GSTe2 -

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Basic information

Entry
Database: PDB / ID: 5ft3
TitleAedes aegypti GSTe2
ComponentsGLUTATHIONE S-TRANSFERASE EPSILON 2
KeywordsTRANSFERASE / GSTE2 / GSH
Function / homology
Function and homology information


glutathione metabolic process / transferase activity
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, 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, 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, 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 / AAEL007951-PA
Similarity search - Component
Biological speciesAEDES AEGYPTI (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.431 Å
AuthorsYunta, C.
CitationJournal: To be Published
Title: A Simple Test for the Determination of Ddt on Sprayed Surfaces
Authors: Yunta, C. / Ismail, H.M. / Paine, M.J.I.
History
DepositionJan 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE EPSILON 2
B: GLUTATHIONE S-TRANSFERASE EPSILON 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0604
Polymers49,4452
Non-polymers6152
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-26.3 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.811, 86.563, 101.021
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 S-TRANSFERASE EPSILON 2


Mass: 24722.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEDES AEGYPTI (yellow fever mosquito) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5PY77
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 1.98 Å3/Da / Density % sol: 37.48 % / Description: NONE
Crystal growDetails: 0.2 M NACL, 0.1 M BIS-TRIS PH 5.7, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.43→28.85 Å / Num. obs: 78165 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 80.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SCALAdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZML

3zml


Resolution: 1.431→27.745 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.174 3912 5 %
Rwork0.1339 --
obs0.1359 78088 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 1.431→27.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 40 584 4052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053560
X-RAY DIFFRACTIONf_angle_d0.964821
X-RAY DIFFRACTIONf_dihedral_angle_d12.2261319
X-RAY DIFFRACTIONf_chiral_restr0.069552
X-RAY DIFFRACTIONf_plane_restr0.005615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.431-1.44840.30921120.21591964X-RAY DIFFRACTION74
1.4484-1.46680.2631250.17992316X-RAY DIFFRACTION87
1.4668-1.48610.24821180.15712461X-RAY DIFFRACTION92
1.4861-1.50640.2271300.14222524X-RAY DIFFRACTION95
1.5064-1.52790.21911490.12452682X-RAY DIFFRACTION99
1.5279-1.55070.19721510.11552604X-RAY DIFFRACTION100
1.5507-1.5750.18791320.10892742X-RAY DIFFRACTION100
1.575-1.60080.1651410.10192639X-RAY DIFFRACTION100
1.6008-1.62840.16861460.10032682X-RAY DIFFRACTION100
1.6284-1.6580.17071430.09562637X-RAY DIFFRACTION100
1.658-1.68990.18531420.09992701X-RAY DIFFRACTION100
1.6899-1.72440.18151420.10382647X-RAY DIFFRACTION100
1.7244-1.76190.14841170.10542721X-RAY DIFFRACTION100
1.7619-1.80280.17381410.11882696X-RAY DIFFRACTION100
1.8028-1.84790.15311540.12162654X-RAY DIFFRACTION100
1.8479-1.89790.20291360.11992695X-RAY DIFFRACTION100
1.8979-1.95370.18711550.12032695X-RAY DIFFRACTION100
1.9537-2.01670.17091330.12212694X-RAY DIFFRACTION100
2.0167-2.08880.15761540.12112667X-RAY DIFFRACTION100
2.0888-2.17240.17041430.12172712X-RAY DIFFRACTION100
2.1724-2.27120.17121420.12032695X-RAY DIFFRACTION100
2.2712-2.39090.1491320.12392725X-RAY DIFFRACTION100
2.3909-2.54060.1871430.13232737X-RAY DIFFRACTION100
2.5406-2.73660.19011490.14532699X-RAY DIFFRACTION100
2.7366-3.01170.1721460.15182742X-RAY DIFFRACTION100
3.0117-3.44680.16061450.14592747X-RAY DIFFRACTION100
3.4468-4.33990.15451440.13712777X-RAY DIFFRACTION99
4.3399-27.750.17531470.16622921X-RAY DIFFRACTION100

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