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- PDB-7so8: Crystal structure of Glutathione S-Transferase from Shrimp Litope... -

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Basic information

Entry
Database: PDB / ID: 7so8
TitleCrystal structure of Glutathione S-Transferase from Shrimp Litopenaeus vannamei in complex with silver ions and a molecules of Glutathione binding in G-site and H-site
ComponentsGlutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / GST / GSH binding in G-site
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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
SILVER ION / GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsEscudero-Garcia, A. / Rudino-Pinera, E. / Miranda-Blancas, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Inhibition of GST class Mu of the shrimp Litopenaeus vannamei by binding silver ions in H-site.
Authors: Escudero-Garcia, A. / Rudino-Pinera, E.
History
DepositionOct 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 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 transferase
C: Glutathione transferase
E: Glutathione transferase
G: Glutathione transferase
H: Glutathione transferase
F: Glutathione transferase
B: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,05522
Polymers204,4208
Non-polymers3,63514
Water20,9331162
1
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0275
Polymers51,1052
Non-polymers9223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0666
Polymers51,1052
Non-polymers9614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-30 kcal/mol
Surface area19240 Å2
MethodPISA
3
E: Glutathione transferase
hetero molecules

F: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1356
Polymers51,1052
Non-polymers1,0304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4420 Å2
ΔGint-39 kcal/mol
Surface area18810 Å2
MethodPISA
4
G: Glutathione transferase
H: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8275
Polymers51,1052
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-30 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 93.020, 169.110
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione transferase / Glutathione S-transferase


Mass: 25552.455 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei (Pacific white shrimp)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q49SB0, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 6.5
Details: 100 mM ammonium sulphate, 100 Bis-Tris pH 6.5, 30% PEG 3350, 300 uM silver nitrate
PH range: 6.5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 12, 2019 / Details: Sagitally focusing 2nd Crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→56.37 Å / Num. obs: 88718 / % possible obs: 98.15 % / Redundancy: 3.104 % / Biso Wilson estimate: 13.76 Å2 / CC1/2: 0.627 / Rmerge(I) obs: 0.6179 / Rpim(I) all: 0.4226 / Rrim(I) all: 0.7511 / Net I/av σ(I): 1.98 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.370.5792.1175300.660.3960.70497.6
2.37-2.610.3973.1176630.8140.2710.48398
2.61-2.990.2664.5176410.9140.1820.32498.2
2.99-3.760.1228.7178490.9830.0840.14998.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26,2018data reduction
XSCALEVERSION Jan 26, 2018data scaling
PHASER7.0.076phasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AN1

5an1


Resolution: 2.2→56.37 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 4472 5.04 %
Rwork0.1914 84236 -
obs0.1949 88708 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.29 Å2 / Biso mean: 16.3226 Å2 / Biso min: 1.6 Å2
Refinement stepCycle: final / Resolution: 2.2→56.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14400 0 219 1162 15781
Biso mean--41.67 18.6 -
Num. residues----1751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.220.31111410.23752792293397
2.22-2.250.3221470.22922727287498
2.25-2.280.29481550.23362832298798
2.28-2.310.29971660.22872754292098
2.31-2.340.31311330.22612748288197
2.34-2.370.31251300.22352815294598
2.37-2.40.30551370.22222797293498
2.4-2.440.31241600.22392762292298
2.44-2.480.28761290.21162847297698
2.48-2.520.28791200.21432789290998
2.52-2.560.31521600.21292747290798
2.56-2.610.29591410.20732890303198
2.61-2.660.25851480.21212732288098
2.66-2.710.2911630.21132776293998
2.71-2.770.27691520.20652784293698
2.77-2.840.31591400.21352851299198
2.84-2.910.30081520.21462794294698
2.91-2.990.29311550.20622800295598
2.99-3.070.30481400.20922820296099
3.07-3.170.29841620.19652829299199
3.17-3.290.24921780.20742762294099
3.29-3.420.29521550.19032856301199
3.42-3.570.23071290.16972857298699
3.57-3.760.23261470.15962816296399
3.76-40.21681720.15362795296799
4-4.310.21131570.13742837299499
4.31-4.740.18221440.13442876302099
4.74-5.420.20211710.14712811298298
5.42-6.830.18961270.18172875300298
6.83-56.370.18581610.18512865302697

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