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- PDB-10pw: Crystal structure of Glutathione Transferase from Shrimp Litopena... -

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Basic information

Entry
Database: PDB / ID: 10pw
TitleCrystal structure of Glutathione Transferase from Shrimp Litopenaeus vannamei in complex with silver ions and a molecules of Glutathione binding in G-site and H-site
ComponentsGlutathione transferase
KeywordsOXIDOREDUCTASE / Glutathione transferase / silver ion inhibition / Marine crustaceans / Litopenaeus vannamei / GSH interaction / enzymatic inhibition
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
SILVER ION / GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEscudero-Garcia, A. / Miranda-Blancas, R. / Rudino-Pinera, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Insights into Silver Ion Inhibition and Dual Glutathione Binding in Glutathione Transferase from the Marine Shrimp Litopenaeus vannamei.
Authors: Escudero-Garcia, A. / Miranda-Blancas, R. / Sotelo-Mundo, R.R. / Rudino-Pinera, E.
History
DepositionJan 31, 2026Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 18, 2026ID: 7SO8
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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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
E: Glutathione transferase
F: Glutathione transferase
G: Glutathione transferase
H: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,40225
Polymers204,4208
Non-polymers3,98317
Water25,0051388
1
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1906
Polymers51,1052
Non-polymers1,0854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-30 kcal/mol
Surface area18940 Å2
MethodPISA
2
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0127
Polymers51,1052
Non-polymers9075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-27 kcal/mol
Surface area19040 Å2
MethodPISA
3
E: Glutathione transferase
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
Buried area4540 Å2
ΔGint-35 kcal/mol
Surface area18940 Å2
MethodPISA
4
G: Glutathione transferase
H: 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 area4250 Å2
ΔGint-34 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 93.020, 169.110
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Glutathione transferase


Mass: 25552.455 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Gluthatione transferase from Litopenaeus vannamei
Source: (gene. exp.) Penaeus vannamei (Pacific white shrimp)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q49SB0, glutathione transferase

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Non-polymers , 6 types, 1405 molecules

#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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

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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: Jan 26, 2018 / Details: SAGITALLY FOCUSING 2ND
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: 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: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 13.76 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.11 / Rrim(I) all: 0.2 / Rsym value: 0.16 / Net I/av σ(I): 6.6 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 8800 / CC star: 0.62 / Rpim(I) all: 0.42 / Rrim(I) all: 0.75 / Rsym value: 0.61 / % possible all: 97.52

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.37 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 4472 5.04 %
Rwork0.192 --
obs0.195 88710 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→56.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14352 0 242 1388 15982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115058
X-RAY DIFFRACTIONf_angle_d1.13920326
X-RAY DIFFRACTIONf_dihedral_angle_d19.4035613
X-RAY DIFFRACTIONf_chiral_restr0.1062119
X-RAY DIFFRACTIONf_plane_restr0.0152590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.29491410.23862792X-RAY DIFFRACTION97
2.22-2.250.3261470.23442727X-RAY DIFFRACTION98
2.25-2.280.30951550.24852832X-RAY DIFFRACTION98
2.28-2.310.29551660.23662754X-RAY DIFFRACTION98
2.31-2.340.32511330.23252748X-RAY DIFFRACTION97
2.34-2.370.33361300.22892815X-RAY DIFFRACTION98
2.37-2.40.29581370.22412797X-RAY DIFFRACTION98
2.4-2.440.27871600.22062762X-RAY DIFFRACTION98
2.44-2.480.28011290.2142847X-RAY DIFFRACTION98
2.48-2.520.27191200.2092789X-RAY DIFFRACTION98
2.52-2.560.30861600.20932747X-RAY DIFFRACTION98
2.56-2.610.24241410.20612890X-RAY DIFFRACTION98
2.61-2.660.25821480.20822732X-RAY DIFFRACTION98
2.66-2.710.26571630.21042776X-RAY DIFFRACTION98
2.71-2.770.26821520.20582784X-RAY DIFFRACTION98
2.77-2.840.26941400.2112851X-RAY DIFFRACTION98
2.84-2.910.25711520.21392794X-RAY DIFFRACTION98
2.91-2.990.25981550.20352800X-RAY DIFFRACTION98
2.99-3.070.26161400.20522820X-RAY DIFFRACTION99
3.07-3.170.26551620.19592829X-RAY DIFFRACTION99
3.17-3.290.23461780.20272762X-RAY DIFFRACTION99
3.29-3.420.2561550.17692856X-RAY DIFFRACTION99
3.42-3.570.21261290.16542857X-RAY DIFFRACTION99
3.57-3.760.20091470.15722816X-RAY DIFFRACTION99
3.76-40.18411720.15252795X-RAY DIFFRACTION99
4-4.310.18411570.13862837X-RAY DIFFRACTION99
4.31-4.740.1871440.13892876X-RAY DIFFRACTION99
4.74-5.420.20211710.15492811X-RAY DIFFRACTION98
5.42-6.830.17081270.19452875X-RAY DIFFRACTION98
6.83-56.370.20921610.19422867X-RAY DIFFRACTION97

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