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- PDB-2imi: Structures of an Insect Epsilon-class Glutathione S-transferase f... -

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Basic information

Entry
Database: PDB / ID: 2imi
TitleStructures of an Insect Epsilon-class Glutathione S-transferase from the Malaria Vector Anopheles Gambiae: Evidence for High DDT-detoxifying Activity
ComponentsEpsilon-class Glutathione S-transferase
KeywordsTRANSFERASE / Epsilon-class Glutathione / S-transferase
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
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 / 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 ...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 / 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 gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWang, Y. / Hemingway, J. / Ranson, H. / Meehan, E.J. / Chen, L.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Structure of an insect epsilon class glutathione S-transferase from the malaria vector Anopheles gambiae provides an explanation for the high DDT-detoxifying activity
Authors: Wang, Y. / Qiu, L. / Ranson, H. / Lumjuan, N. / Hemingway, J. / Setzer, W.N. / Meehan, E.J. / Chen, L.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE TWO CLOSEST MATCHES IN SEQUENCE DATABASES, UNP Q7PVS6_ANOGA AND GB EAA43411 HAVE ... SEQUENCE TWO CLOSEST MATCHES IN SEQUENCE DATABASES, UNP Q7PVS6_ANOGA AND GB EAA43411 HAVE CONFLICTS WITH SEQUENCE AS SEEN IN THE ELECTRON DENSITY MAPS: Q7PVS6_ANOGA HAS ADDITIONAL N-TERMINAL LYSINE EAA43411 HAS ADDITIONAL C-TERMINAL LYSINE AND ALANINE (REPORTED HERE AS INSERTIONS)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epsilon-class Glutathione S-transferase
B: Epsilon-class Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3744
Polymers49,7592
Non-polymers6152
Water7,584421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.065, 83.793, 92.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

21A-256-

HOH

31A-263-

HOH

41A-345-

HOH

DetailsThe biological assembly is a dimer

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Components

#1: Protein Epsilon-class Glutathione S-transferase / E.C.2.5.1.18 / glutathione S-transferase E2


Mass: 24879.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: AF316636 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7PVS6, glutathione transferase
#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.: 421 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M amonium acetate, 0.1M sodium acetate pH4.6 and 30% w/v Polyethylene Glycerol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2006
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 6.5 % / Av σ(I) over netI: 10 / Number: 491866 / Rmerge(I) obs: 0.089 / Χ2: 0.98 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 76216 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.025099.810.0571.0426.6
2.393.0210010.0751.0136.9
2.092.3910010.0951.256.9
1.92.0910010.1221.1387
1.761.910010.1671.1656.9
1.661.7610010.2281.0016.8
1.581.6610010.3030.8836.8
1.511.5810010.3620.7746.4
1.451.5110010.4370.6895.7
1.41.4510010.5170.6394.7
ReflectionResolution: 1.4→50 Å / Num. all: 76216 / Num. obs: 76216 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Χ2: 0.981 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 10 / Num. unique all: 7519 / Rsym value: 0.028 / Χ2: 0.639 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2IL3

2il3


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.932 / SU ML: 0.038 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3803 5 %RANDOM
Rwork0.174 ---
all0.175 75783 --
obs0.175 75783 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 40 421 3948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223601
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9934877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.195438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03124.545154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71315635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6581516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022682
X-RAY DIFFRACTIONr_nbd_refined0.2010.21742
X-RAY DIFFRACTIONr_nbtor_refined0.310.22494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.236
X-RAY DIFFRACTIONr_mcbond_it0.6671.52245
X-RAY DIFFRACTIONr_mcangle_it1.17623567
X-RAY DIFFRACTIONr_scbond_it2.07331494
X-RAY DIFFRACTIONr_scangle_it3.024.51310
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 255 -
Rwork0.214 5242 -
obs-5497 99.95 %

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