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- PDB-4yav: Crystal structure of LigG in complex with B-glutathionyl-acetover... -

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Basic information

Entry
Database: PDB / ID: 4yav
TitleCrystal structure of LigG in complex with B-glutathionyl-acetoveratrone (GS-AV) from Sphingobium sp. strain SYK-6
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GSH-lyase GSH-dependent
Function / homology
Function and homology information


transferase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
Chem-GAZ / Glutathione S-transferase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.401 Å
AuthorsPereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Authors: Pereira, J.H. / Heins, R.A. / Gall, D.L. / McAndrew, R.P. / Deng, K. / Holland, K.C. / Donohue, T.J. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Adams, P.D.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3543
Polymers30,7731
Non-polymers5822
Water6,017334
1
A: Glutathione S-transferase
hetero molecules

A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7086
Polymers61,5452
Non-polymers1,1634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2840 Å2
ΔGint-44 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.543, 64.543, 120.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-708-

HOH

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Components

#1: Protein Glutathione S-transferase


Mass: 30772.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligG, SLG_08670 / Production host: Escherichia coli (E. coli) / References: UniProt: G2IN94
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GAZ / L-gamma-glutamyl-3-{(E)-[2-(3,4-dimethoxyphenyl)-2-oxoethylidene]-lambda~4~-sulfanyl}-L-alanylglycine


Mass: 485.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O9S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris propane pH 7.0, 1.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.4→41.037 Å / Num. obs: 58125 / % possible obs: 100 % / Redundancy: 10.8 % / Net I/σ(I): 23.8

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.401→41.037 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1642 2003 3.45 %
Rwork0.1393 --
obs0.1402 58064 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→41.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 38 334 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132227
X-RAY DIFFRACTIONf_angle_d1.5583019
X-RAY DIFFRACTIONf_dihedral_angle_d19.223849
X-RAY DIFFRACTIONf_chiral_restr0.089305
X-RAY DIFFRACTIONf_plane_restr0.009396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.401-1.43550.24091380.18533962X-RAY DIFFRACTION100
1.4355-1.47440.21661380.16123935X-RAY DIFFRACTION100
1.4744-1.51770.18981390.14543929X-RAY DIFFRACTION100
1.5177-1.56670.17831420.13483989X-RAY DIFFRACTION100
1.5667-1.62270.1941410.12973935X-RAY DIFFRACTION100
1.6227-1.68770.17691430.12463968X-RAY DIFFRACTION100
1.6877-1.76450.1791360.12553975X-RAY DIFFRACTION100
1.7645-1.85750.15051460.12394004X-RAY DIFFRACTION100
1.8575-1.97390.14461420.13093974X-RAY DIFFRACTION100
1.9739-2.12630.17131430.13023999X-RAY DIFFRACTION100
2.1263-2.34030.15121450.12734013X-RAY DIFFRACTION100
2.3403-2.67890.17611470.13834059X-RAY DIFFRACTION100
2.6789-3.37490.16791480.14944073X-RAY DIFFRACTION100
3.3749-41.05450.14731550.14554246X-RAY DIFFRACTION100

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