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- PDB-3zml: Anopheles funestus glutathione-s-transferase epsilon 2 (GSTe2) pr... -

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Basic information

Entry
Database: PDB / ID: 3zml
TitleAnopheles funestus glutathione-s-transferase epsilon 2 (GSTe2) protein structure from different alelles: A single amino acid change confers high level of DDT resistance and cross resistance to permethrin in a major malaria vector in Africa
ComponentsGLUTATHIONE S-TRANSFERASE E2
KeywordsTRANSFERASE
Function / homology
Function and homology information


glutathione transferase / 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 / glutathione transferase
Similarity search - Component
Biological speciesANOPHELES FUNESTUS (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.639 Å
AuthorsYunta, C. / Albert, A.
CitationJournal: Genome Biol. / Year: 2014
Title: A Single Mutation in the Gste2 Gene Allows Tracking of Metabolically-Based Insecticide Resistance in a Major Malaria Vector.
Authors: Riveron, J.M. / Yunta, C. / Ibrahim, S.S. / Djouaka, R. / Irving, H. / Menze, B.D. / Ismail, H.M. / Hemingway, J. / Ranson, H. / Albert, A. / Wondji, C.S.
History
DepositionFeb 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE E2
B: GLUTATHIONE S-TRANSFERASE E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1814
Polymers50,5662
Non-polymers6152
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-23 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.250, 73.040, 129.650
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 E2 / GLUTATHIONE-S-TRANSFERASE EPSILON 2 / GSTE2


Mass: 25283.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANOPHELES FUNESTUS (African malaria mosquito)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0XSZ1
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.33 Å3/Da / Density % sol: 47.29 % / Description: NONE
Crystal growDetails: 25% W/V PEG 1500 AND 0.1M PCB, BUFFER PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.64→32.48 Å / Num. obs: 58184 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 12.77 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IMI

2imi


Resolution: 1.639→32.484 Å / SU ML: 0.4 / σ(F): 1.05 / Phase error: 18.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2131 5416 5.1 %
Rwork0.1878 --
obs0.1891 57924 96.19 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.94 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0539 Å20 Å20 Å2
2--0.2149 Å20 Å2
3---0.839 Å2
Refinement stepCycle: LAST / Resolution: 1.639→32.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 40 577 4100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213595
X-RAY DIFFRACTIONf_angle_d1.9414863
X-RAY DIFFRACTIONf_dihedral_angle_d14.6481357
X-RAY DIFFRACTIONf_chiral_restr0.333547
X-RAY DIFFRACTIONf_plane_restr0.012625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.639-1.65760.32991530.24553263X-RAY DIFFRACTION93
1.6576-1.67710.30011720.24353328X-RAY DIFFRACTION95
1.6771-1.69760.26691830.2183311X-RAY DIFFRACTION93
1.6976-1.71910.25861690.2213280X-RAY DIFFRACTION95
1.7191-1.74170.30292010.20553315X-RAY DIFFRACTION95
1.7417-1.76550.25782290.20263280X-RAY DIFFRACTION94
1.7655-1.79080.23511650.19983307X-RAY DIFFRACTION95
1.7908-1.81750.22662030.19043328X-RAY DIFFRACTION95
1.8175-1.84590.19791780.18063291X-RAY DIFFRACTION95
1.8459-1.87620.22091690.17623398X-RAY DIFFRACTION95
1.8762-1.90850.22911560.24663310X-RAY DIFFRACTION94
1.9085-1.94320.47641860.47553155X-RAY DIFFRACTION91
1.9432-1.98060.24391670.19913407X-RAY DIFFRACTION95
1.9806-2.0210.20441810.16893315X-RAY DIFFRACTION96
2.021-2.06490.22231830.18323341X-RAY DIFFRACTION95
2.0649-2.1130.22261680.17623388X-RAY DIFFRACTION96
2.113-2.16580.19462000.15533382X-RAY DIFFRACTION96
2.1658-2.22430.19761570.1793399X-RAY DIFFRACTION97
2.2243-2.28980.34561510.34853244X-RAY DIFFRACTION92
2.2898-2.36370.19321630.15373439X-RAY DIFFRACTION97
2.3637-2.44810.17131740.15043491X-RAY DIFFRACTION98
2.4481-2.54610.2171800.15453393X-RAY DIFFRACTION98
2.5461-2.66190.19261980.16753463X-RAY DIFFRACTION98
2.6619-2.80220.20811940.16993448X-RAY DIFFRACTION99
2.8022-2.97760.19281770.1683474X-RAY DIFFRACTION99
2.9776-3.20740.19232060.16693477X-RAY DIFFRACTION99
3.2074-3.52980.17561870.15623518X-RAY DIFFRACTION100
3.5298-4.03970.17251890.15813496X-RAY DIFFRACTION100
4.0397-5.08650.14082000.13873481X-RAY DIFFRACTION100
5.0865-32.490.1751770.17313527X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -8.321 Å / Origin y: -1.0119 Å / Origin z: -14.7124 Å
111213212223313233
T0.0004 Å20.0003 Å20.0033 Å2--0.0012 Å2-0.0142 Å2---0.0013 Å2
L0.0003 °20.0003 °2-0.0002 °2-0.0006 °20.0008 °2--0.0007 °2
S-0.0045 Å °-0.0012 Å °0.002 Å °-0.0007 Å °-0.0001 Å °0.0006 Å °0.002 Å °-0.0001 Å °0 Å °
Refinement TLS groupSelection details: ALL

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