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- PDB-4top: Glycine max glutathione transferase -

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Basic information

Entry
Database: PDB / ID: 4top
TitleGlycine max glutathione transferase
Components2,4-D inducible glutathione S-transferase
KeywordsTRANSFERASE / INDUCED-FIT MECHANISM / TAU CLASS GST
Function / homology
Function and homology information


response to chemical / 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 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-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 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
GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
AuthorsAxarli, I. / Dhavala, P. / Papageorgiou, A.C.
Citation
Journal: To Be Published
Title: Comparative analysis of the structural and functional features of two homologous tau class glutathione transferases from Glycine max
Authors: Skopelitou, K. / Muleta, A. / Papageorgiou, A.C. / Pavli, O. / Flemetakis, E. / Chronopoulou, E. / Skaracis, G. / Labrou, N.
#1: Journal: Biochem. J. / Year: 2009
Title: Crystal structure of Glycine max glutathione transferase in complex with glutathione: investigation of the mechanism operating by the Tau class glutathione transferases.
Authors: Axarli, I. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: PDBE
SupersessionJun 25, 2014ID: 3FHS / Details: Rerefinement
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Other
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,4-D inducible glutathione S-transferase
B: 2,4-D inducible glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8944
Polymers51,2792
Non-polymers6152
Water3,261181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-20 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.262, 136.262, 90.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein 2,4-D inducible glutathione S-transferase


Mass: 25639.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: GSTa / Production host: Escherichia coli (E. coli) / References: UniProt: O49235, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.73 Å3/Da / Density % sol: 73.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: TRI-SODIUM CITRATE 1.2-1.3M IN HEPES BUFFER 0.1M, PH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2007
RadiationMonochromator: FIXED-EXIT SAGITAL FOCUSING DOUBLE SILICON (111) CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 2.35→19.7 Å / Num. obs: 39774 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.49 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSDecember 2013data reduction
XSCALEDecember 2013data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vo4

2vo4


Resolution: 2.351→19.65 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 2039 5.13 %Random selection
Rwork0.1977 ---
obs0.1998 39759 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.351→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 40 181 3827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013788
X-RAY DIFFRACTIONf_angle_d1.3045124
X-RAY DIFFRACTIONf_dihedral_angle_d17.0821488
X-RAY DIFFRACTIONf_chiral_restr0.049538
X-RAY DIFFRACTIONf_plane_restr0.007653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3514-2.4060.3881360.33872485X-RAY DIFFRACTION99
2.406-2.46610.37571370.32842491X-RAY DIFFRACTION100
2.4661-2.53260.3331380.31732503X-RAY DIFFRACTION100
2.5326-2.6070.30291340.28932505X-RAY DIFFRACTION100
2.607-2.69090.30691370.28252509X-RAY DIFFRACTION100
2.6909-2.78680.29071360.26822505X-RAY DIFFRACTION100
2.7868-2.89810.3161130.26192516X-RAY DIFFRACTION100
2.8981-3.02950.28191450.24732537X-RAY DIFFRACTION100
3.0295-3.18860.26731410.23782482X-RAY DIFFRACTION100
3.1886-3.38750.29731420.2112514X-RAY DIFFRACTION100
3.3875-3.64750.24651340.17822521X-RAY DIFFRACTION100
3.6475-4.01170.21291310.16852523X-RAY DIFFRACTION100
4.0117-4.58580.19461460.15262507X-RAY DIFFRACTION100
4.5858-5.75340.19031500.1542537X-RAY DIFFRACTION100
5.7534-19.65110.18671190.16252585X-RAY DIFFRACTION99

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