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- PDB-7rhp: Crystal Structure of Honeybee (Apis mellifera) glutathione S-tran... -

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Basic information

Entry
Database: PDB / ID: 7rhp
TitleCrystal Structure of Honeybee (Apis mellifera) glutathione S-transferase AmGSTD1
ComponentsGlutathione S-transferase AmGSTD1
KeywordsTRANSFERASE / glutathione s-transferase / GSH / delta / honeybee / Apis mellifera / complex
Function / homology
Function and homology information


glutathione transferase activity / glutathione metabolic process
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 / Glutathione S-transferase D1 isoform X1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
Model detailscomplex with GSH
AuthorsMoural, T.W. / Zhu, F.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA) United States
CitationJournal: Chemosphere / Year: 2023
Title: Architecture and potential roles of a delta-class glutathione S-transferase in protecting honey bee from agrochemicals.
Authors: Moural, T.W. / Koirala B K, S. / Bhattarai, G. / He, Z. / Guo, H. / Phan, N.T. / Rajotte, E.G. / Biddinger, D.J. / Hoover, K. / Zhu, F.
History
DepositionJul 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 17, 2024Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase AmGSTD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6392
Polymers29,3321
Non-polymers3071
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.090, 60.090, 232.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

21A-543-

HOH

31A-547-

HOH

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Components

#1: Protein Glutathione S-transferase AmGSTD1


Mass: 29331.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: 409490 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A7M7GUY7
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.2 M Sodium chloride, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.54→52.04 Å / Num. obs: 37014 / % possible obs: 95 % / Redundancy: 16.9 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07798 / Rpim(I) all: 0.01925 / Rrim(I) all: 0.08041 / Net I/σ(I): 14.34
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.9732 / Mean I/σ(I) obs: 0.34 / Num. unique obs: 2976 / CC1/2: 0.772 / CC star: 0.933 / Rpim(I) all: 0.2854 / % possible all: 73.91

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.78 Å52.04 Å
Translation4.78 Å52.04 Å

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Processing

Software
NameVersionClassification
xia2data scaling
PHASER2.8.3phasing
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WYW

3wyw


Resolution: 1.54→52.04 Å / SU ML: 0.1617 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.5595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 1666 4.62 %
Rwork0.1902 34382 -
obs0.1907 36048 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.21 Å2
Refinement stepCycle: LAST / Resolution: 1.54→52.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 20 174 1942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061825
X-RAY DIFFRACTIONf_angle_d0.87872468
X-RAY DIFFRACTIONf_chiral_restr0.0483265
X-RAY DIFFRACTIONf_plane_restr0.0047316
X-RAY DIFFRACTIONf_dihedral_angle_d6.2541243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.31951030.25722115X-RAY DIFFRACTION72.2
1.59-1.640.25731230.22942530X-RAY DIFFRACTION86.28
1.64-1.690.25781330.23252751X-RAY DIFFRACTION93.55
1.69-1.760.20621390.22762843X-RAY DIFFRACTION95.82
1.76-1.840.27181350.222858X-RAY DIFFRACTION97.02
1.84-1.940.24661430.21332930X-RAY DIFFRACTION97.9
1.94-2.060.21061430.19552927X-RAY DIFFRACTION98.49
2.06-2.220.23731460.1882978X-RAY DIFFRACTION99.08
2.22-2.440.20161440.17572986X-RAY DIFFRACTION99.46
2.44-2.80.20691470.18243035X-RAY DIFFRACTION99.53
2.8-3.520.18471490.17663113X-RAY DIFFRACTION99.88
3.53-52.040.17991610.18823316X-RAY DIFFRACTION99.37

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