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- PDB-7rka: Crystal structure analysis of Colorado potato beetle glutathione-... -

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Basic information

Entry
Database: PDB / ID: 7rka
TitleCrystal structure analysis of Colorado potato beetle glutathione-S transferase LdGSTu1
Componentsglutathione S-transferase u1
KeywordsTRANSFERASE / glutathione s-transferase / GSH / unclassified / Colorado potato beetle / Imidocloprid resistant / Leptinotarsa decemlineata / complex / glutathione
Function / homology
Function and homology information


glutathione metabolic process / transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Putative glutathione S-transferase uncharacterized class member 1
Similarity search - Component
Biological speciesLeptinotarsa decemlineata (Colorado potato beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailsLdGSTu1 structure complex with GSH
AuthorsMoural, T.W. / Zhu, F.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA) United States
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Functional Characterization of One Unclassified Glutathione S-Transferase in Xenobiotic Adaptation of Leptinotarsa decemlineata.
Authors: Liu, Y. / Moural, T. / Koirala B K, S. / Hernandez, J. / Shen, Z. / Alyokhin, A. / Zhu, F.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutathione S-transferase u1
B: glutathione S-transferase u1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2083
Polymers52,9002
Non-polymers3071
Water5,711317
1
A: glutathione S-transferase u1
hetero molecules

A: glutathione S-transferase u1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5154
Polymers52,9002
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3930 Å2
ΔGint-28 kcal/mol
Surface area18180 Å2
MethodPISA
2
B: glutathione S-transferase u1

B: glutathione S-transferase u1


Theoretical massNumber of molelcules
Total (without water)52,9002
Polymers52,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.452, 46.440, 87.192
Angle α, β, γ (deg.)90.000, 91.350, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein glutathione S-transferase u1


Mass: 26450.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptinotarsa decemlineata (Colorado potato beetle)
Plasmid: pET9Bc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta II (DE3) / References: UniProt: A0A1P8PEY0, glutathione transferase
#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.: 317 / 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: 2.29 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 0.1 M MES, pH 6.5, 0.2 M sodium chloride, 20% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→29.22 Å / Num. obs: 42482 / % possible obs: 97.12 % / Redundancy: 3.2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04433 / Rpim(I) all: 0.0286 / Rrim(I) all: 0.05293 / Net I/σ(I): 16.28
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 3476 / CC1/2: 0.888 / CC star: 0.97 / Rpim(I) all: 0.2128 / Rrim(I) all: 0.3295 / % possible all: 79.63

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5ZFG

5zfg


Resolution: 1.8→29.22 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 1741 4.1 %
Rwork0.1594 40734 -
obs0.1604 42475 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.85 Å2 / Biso mean: 29.8809 Å2 / Biso min: 8.92 Å2
Refinement stepCycle: final / Resolution: 1.8→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 35 317 3768
Biso mean--43.91 35.12 -
Num. residues----422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.26331090.22572717282678
1.85-1.910.23021390.19833143328291
1.91-1.980.21311430.18153392353598
1.98-2.060.21371480.170934793627100
2.06-2.150.1981520.160234633615100
2.15-2.270.19721430.156334603603100
2.27-2.410.18881520.150735113663100
2.41-2.60.17761510.149734543605100
2.6-2.860.17841480.154234753623100
2.86-3.270.15851460.148435133659100
3.27-4.120.15891540.145335193673100
4.12-29.220.18551560.169636083764100

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