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- PDB-7ebu: Crystal structure of Aedes aegypti Noppera-bo, glutathione S-tran... -

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Basic information

Entry
Database: PDB / ID: 7ebu
TitleCrystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in Daidzein- and glutathione-bound form
ComponentsGlutathione transferase
KeywordsTRANSFERASE / Glutathione / Glutathione S-transferase / GST
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / 7-hydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one / glutathione transferase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsInaba, K. / Koiwai, K. / Senda, M. / Senda, T. / Niwa, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K19163 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)25712010 Japan
Japan Agency for Medical Research and Development (AMED)20am0101001 Japan
CitationJournal: Bmc Biol. / Year: 2022
Title: Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.
Authors: Inaba, K. / Ebihara, K. / Senda, M. / Yoshino, R. / Sakuma, C. / Koiwai, K. / Takaya, D. / Watanabe, C. / Watanabe, A. / Kawashima, Y. / Fukuzawa, K. / Imamura, R. / Kojima, H. / Okabe, T. / ...Authors: Inaba, K. / Ebihara, K. / Senda, M. / Yoshino, R. / Sakuma, C. / Koiwai, K. / Takaya, D. / Watanabe, C. / Watanabe, A. / Kawashima, Y. / Fukuzawa, K. / Imamura, R. / Kojima, H. / Okabe, T. / Uemura, N. / Kasai, S. / Kanuka, H. / Nishimura, T. / Watanabe, K. / Inoue, H. / Fujikawa, Y. / Honma, T. / Hirokawa, T. / Senda, T. / Niwa, R.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
B: Glutathione transferase
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,84520
Polymers104,2784
Non-polymers2,56716
Water13,709761
1
A: Glutathione transferase
hetero molecules

A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,50312
Polymers52,1392
Non-polymers1,36410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454y-1/2,x+1/2,-z-1/21
Buried area2600 Å2
ΔGint-18 kcal/mol
Surface area18200 Å2
MethodPISA
2
B: Glutathione transferase
hetero molecules

B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3428
Polymers52,1392
Non-polymers1,2036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area2820 Å2
ΔGint-19 kcal/mol
Surface area18590 Å2
MethodPISA
3
C: Glutathione transferase
hetero molecules

D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42310
Polymers52,1392
Non-polymers1,2838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-y+1/2,x,z-1/41
Buried area2550 Å2
ΔGint-22 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.213, 152.213, 146.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein
Glutathione transferase


Mass: 26069.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: 5569853
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1S4FIB3
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZF1 / 7-hydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one


Mass: 254.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32.5%(w/v) PEG 4000, 0.5 M CaCl2, 0.1 M Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.13 Å / Num. obs: 62167 / % possible obs: 99.5 % / Redundancy: 26.5 % / Biso Wilson estimate: 26.11 Å2 / Rpim(I) all: 0.025 / Net I/σ(I): 22
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 4293 / Rpim(I) all: 0.235

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KEM

6kem


Resolution: 1.95→48.13 Å / SU ML: 0.2495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 3151 5.1 %
Rwork0.1901 58634 -
obs0.193 61785 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 164 761 7619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767071
X-RAY DIFFRACTIONf_angle_d0.97979646
X-RAY DIFFRACTIONf_chiral_restr0.05561121
X-RAY DIFFRACTIONf_plane_restr0.00931230
X-RAY DIFFRACTIONf_dihedral_angle_d13.87522519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.28811300.21822515X-RAY DIFFRACTION98.4
1.98-2.010.26291250.21172511X-RAY DIFFRACTION98.54
2.01-2.040.30541070.21232544X-RAY DIFFRACTION98.62
2.04-2.080.4069880.32692491X-RAY DIFFRACTION95.34
2.08-2.120.29171220.22322519X-RAY DIFFRACTION98.4
2.12-2.160.29011290.22172512X-RAY DIFFRACTION98.66
2.16-2.20.32551320.2252550X-RAY DIFFRACTION99.04
2.2-2.250.36041160.26332537X-RAY DIFFRACTION97.75
2.25-2.30.36611220.22942467X-RAY DIFFRACTION96.71
2.3-2.360.25721370.19552533X-RAY DIFFRACTION99.18
2.36-2.420.28641400.19612542X-RAY DIFFRACTION99.04
2.42-2.490.29791640.20212520X-RAY DIFFRACTION98.93
2.49-2.570.27131480.20152518X-RAY DIFFRACTION98.78
2.57-2.670.27411460.2092530X-RAY DIFFRACTION98.38
2.67-2.770.241390.20852550X-RAY DIFFRACTION98.82
2.77-2.90.27191630.19792527X-RAY DIFFRACTION99.23
2.9-3.050.23811540.19612550X-RAY DIFFRACTION99.48
3.05-3.240.22981590.18452550X-RAY DIFFRACTION99.09
3.24-3.490.2291650.17892537X-RAY DIFFRACTION98.69
3.49-3.840.19771500.15822582X-RAY DIFFRACTION99.02
3.84-4.40.19571430.14762603X-RAY DIFFRACTION99.28
4.4-5.540.17631170.15952673X-RAY DIFFRACTION99.82
5.54-48.130.23581550.18242773X-RAY DIFFRACTION99.8

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