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- PDB-4g0l: Glutathionyl-hydroquinone Reductase, YqjG, of E.coli complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4g0l
TitleGlutathionyl-hydroquinone Reductase, YqjG, of E.coli complexed with GSH
Componentsprotein yqjG
KeywordsOXIDOREDUCTASE / glutathionyl-hydroquinone reductase
Function / homology
Function and homology information


glutathionyl-hydroquinone reductase / oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / glutathione transferase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Glutathione S-transferase Omega/GSH / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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, N-terminal ...Glutathione S-transferase Omega/GSH / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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, 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 / Glutathionyl-hydroquinone reductase YqjG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsGreen, A.R. / Hayes, R.P. / Xun, L. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural understanding of the glutathione-dependent reduction mechanism of glutathionyl-hydroquinone reductases.
Authors: Green, A.R. / Hayes, R.P. / Xun, L. / Kang, C.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: protein yqjG
B: protein yqjG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,01519
Polymers74,8602
Non-polymers2,15517
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-242 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.791, 148.791, 108.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein protein yqjG


Mass: 37429.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3102, JW3073, yqjG / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42620
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 4.62 Å3/Da / Density % sol: 73.4 %
Crystal growTemperature: 277.15 K / pH: 6.5
Details: 0.1M MES monohydrate, 1.6M ammonium sulfate, 10% 1,4-dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→49.9 Å / Num. obs: 40245 / % possible obs: 60.4 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.55→2.59 Å / % possible all: 60.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→49.9 Å / SU ML: 0.37 / σ(F): 0.24 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1925 4.78 %
Rwork0.179 --
obs0.181 40245 96 %
all-41935 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.97 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1211 Å20 Å20 Å2
2--0.1211 Å20 Å2
3----0.2421 Å2
Refinement stepCycle: LAST / Resolution: 2.62→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5278 0 122 122 5522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065608
X-RAY DIFFRACTIONf_angle_d1.0337637
X-RAY DIFFRACTIONf_dihedral_angle_d15.4281987
X-RAY DIFFRACTIONf_chiral_restr0.075780
X-RAY DIFFRACTIONf_plane_restr0.004967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6193-2.68480.32441270.24632397X-RAY DIFFRACTION86
2.6848-2.75740.33261300.22082527X-RAY DIFFRACTION89
2.7574-2.83850.27581210.21542574X-RAY DIFFRACTION92
2.8385-2.93010.27951350.22012641X-RAY DIFFRACTION93
2.9301-3.03480.3191370.22342687X-RAY DIFFRACTION96
3.0348-3.15630.26531380.21412725X-RAY DIFFRACTION97
3.1563-3.30.22111390.1972777X-RAY DIFFRACTION97
3.3-3.47390.23571390.18262777X-RAY DIFFRACTION98
3.4739-3.69150.22211430.17792793X-RAY DIFFRACTION99
3.6915-3.97640.20121380.15792829X-RAY DIFFRACTION99
3.9764-4.37630.19431450.14872861X-RAY DIFFRACTION99
4.3763-5.00910.17021420.13292839X-RAY DIFFRACTION100
5.0091-6.30890.20891410.16322899X-RAY DIFFRACTION100
6.3089-49.93840.18481500.16922994X-RAY DIFFRACTION100

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