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- PDB-5g5e: Crystallographic structure of the Tau class glutathione S-transfe... -

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Basic information

Entry
Database: PDB / ID: 5g5e
TitleCrystallographic structure of the Tau class glutathione S-transferase MiGSTU from mango Mangifera indica L.
ComponentsTAU CLASS GLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / TAU CLASS / MANGO / DETOXIFICATION.
Function / homology
Function and homology information


toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / glutathione transferase
Similarity search - Component
Biological speciesMANGIFERA INDICA (mango)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsValenzuela-Chavira, I. / Serrano-Posada, H. / Lopez-Zavala, A. / Hernandez-Paredes, J. / Sotelo-Mundo, R.
CitationJournal: Biochimie / Year: 2017
Title: Insights Into Ligand Binding to a Glutathione S-Transferase from Mango: Structure, Thermodynamics and Kinetics
Authors: Valenzuela-Chavira, I. / Contreras-Vergara, C.A. / Arvizu-Flores, A.A. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Hernandez-Paredes, J. / Rudino-Pinera, E. / ...Authors: Valenzuela-Chavira, I. / Contreras-Vergara, C.A. / Arvizu-Flores, A.A. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Hernandez-Paredes, J. / Rudino-Pinera, E. / Stojanoff, V. / Sotelo-Mundo, R.R. / Islas-Osuna, M.A.
History
DepositionMay 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Jun 6, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TAU CLASS GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9285
Polymers25,5511
Non-polymers3774
Water7,350408
1
A: TAU CLASS GLUTATHIONE S-TRANSFERASE
hetero molecules

A: TAU CLASS GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,85610
Polymers51,1012
Non-polymers7558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4190 Å2
ΔGint-2 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.162, 49.414, 53.348
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2038-

HOH

21A-2104-

HOH

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Components

#1: Protein TAU CLASS GLUTATHIONE S-TRANSFERASE


Mass: 25550.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MANGIFERA INDICA (mango)
Description: THE MIGSTU SEQUENCE WAS IDENTIFIED FROM A MANGO HADEN MESOCARP CDNA SHOTGUN-CDNA SEQUENCING PROJECT.
Plasmid: PJEXPRESS404 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1P8NWC2*PLUS, glutathione transferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.22 Å3/Da / Density % sol: 44.56 % / Description: NONE
Crystal growpH: 6
Details: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 6.0, 25%(W/V) POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: BRUKER / Detector: CMOS / Date: May 12, 2015 / Details: HELIOS MX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→22.3 Å / Num. obs: 20863 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 10.02 Å2 / Rmerge(I) obs: 0.33 / Net I/σ(I): 28
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 16.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PROTEUM2data reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON THE STRUCTURE OF WHEAT TAU CLASS GLUTATHIONE S-TRANSFERASE. PDB ENTRY 1GWC.

1gwc


Resolution: 1.8→22.312 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2037 5 %
Rwork0.1612 --
obs0.1626 20863 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 25 408 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091865
X-RAY DIFFRACTIONf_angle_d1.232529
X-RAY DIFFRACTIONf_dihedral_angle_d13.192697
X-RAY DIFFRACTIONf_chiral_restr0.047276
X-RAY DIFFRACTIONf_plane_restr0.006320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84190.26041350.21982600X-RAY DIFFRACTION100
1.8419-1.88790.2291340.19582532X-RAY DIFFRACTION100
1.8879-1.93890.21971350.1972598X-RAY DIFFRACTION100
1.9389-1.99590.27451350.17732545X-RAY DIFFRACTION100
1.9959-2.06030.23151350.17722591X-RAY DIFFRACTION100
2.0603-2.13390.21031370.16792591X-RAY DIFFRACTION100
2.1339-2.21930.20991370.16662560X-RAY DIFFRACTION100
2.2193-2.32020.1751350.16152564X-RAY DIFFRACTION100
2.3202-2.44240.19961330.15952546X-RAY DIFFRACTION100
2.4424-2.59520.19111390.15522589X-RAY DIFFRACTION100
2.5952-2.79520.18431360.16222572X-RAY DIFFRACTION100
2.7952-3.07580.17891340.15822553X-RAY DIFFRACTION100
3.0758-3.51940.17541370.14832573X-RAY DIFFRACTION100
3.5194-4.42840.13271380.13512567X-RAY DIFFRACTION100
4.4284-22.31350.17451370.14792574X-RAY DIFFRACTION100

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