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- PDB-1r5a: Glutathione S-transferase -

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Basic information

Entry
Database: PDB / ID: 1r5a
TitleGlutathione S-transferase
Componentsglutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / Glutathione S-transferase / GST / Glutathione / GSH / MOSQUITO / DETOXIFICATION / XENOBIOTICS
Function / homology
Function and homology information


glutathione metabolic process / transferase activity / metal ion binding
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / GLUTATHIONE SULFONIC ACID / Glutathione transferase
Similarity search - Component
Biological speciesAnopheles cracens (mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOakley, A.J.
Citation
Journal: Biochem.J. / Year: 2005
Title: Identification, characterization and structure of a new Delta class glutathione transferase isoenzyme.
Authors: Udomsinprasert, R. / Pongjaroenkit, S. / Wongsantichon, J. / Oakley, A.J. / Prapanthadara, L.A. / Wilce, M.C. / Ketterman, A.J.
#1: Journal: Protein Sci. / Year: 2001
Title: The crystal structures of glutathione S-transferases isozymes 1-3 and 1-4 from Anopheles dirus species B.
Authors: Oakley, A.J. / Harnnoi, T. / Udomsinprasert, R. / Jirajaroenrat, K. / Ketterman, A.J. / Wilce, M.C.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 25, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6105
Polymers25,0641
Non-polymers5464
Water79344
1
A: glutathione transferase
hetero molecules

A: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,22010
Polymers50,1282
Non-polymers1,0928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Unit cell
Length a, b, c (Å)122.129, 122.129, 74.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1008-

HOH

21A-1022-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: X, -Y + 1/2, -Z +1/4

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Components

#1: Protein glutathione transferase / Glutathione S-transferase / glutathione S-transferase 1-5


Mass: 25063.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles cracens (mosquito) / Gene: adGST1-5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GQG7, glutathione transferase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O9S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.75M lithium sulfate, 0.1M potassium phosphate, 1mM Copper (II) chloride, 10mM glutathione-sulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.6-2 M1reservoirLi2SO4
21 mM1reservoirCuCl2
3100 mMsodium phosphate1reservoirpH6.5-7.5
413.1 mg/mlprotein1drop
510 mMglutathione sulphonic acid1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2001 / Details: Nickle mirrors
RadiationMonochromator: Nickle mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 10052 / Num. obs: 9605 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1101 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 37582
Reflection shell
*PLUS
% possible obs: 97.9 % / Num. unique obs: 963 / Num. measured obs: 3682

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2A

1v2a


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 457 -RANDOM
Rwork0.233 ---
all-9602 --
obs-9602 95.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.1 Å20 Å20 Å2
2---14.1 Å20 Å2
3---28.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 26 44 1801
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.045
RfactorNum. reflection% reflection
Rfree0.407 81 -
Rwork0.351 --
obs-1612 97.5 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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