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- PDB-4g0i: Glutathionyl-Hydroquinone Reductase, YqjG of Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4g0i
TitleGlutathionyl-Hydroquinone Reductase, YqjG of Escherichia coli
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
Glutathionyl-hydroquinone reductase YqjG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)76,59817
Polymers74,8602
Non-polymers1,73815
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-156 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.147, 149.147, 105.340
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 4.52 Å3/Da / Density % sol: 72.78 %
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: Apr 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→48.8 Å / Num. obs: 74305 / % possible obs: 86.4 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.05→2.09 Å / % possible all: 73.5

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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: 2.05→48.8 Å / SU ML: 0.28 / σ(F): 0.11 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1753 2.37 %
Rwork0.196 --
obs0.196 74035 87.4 %
all-84714 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.78 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3662 Å2-0 Å2-0 Å2
2--2.3662 Å2-0 Å2
3----4.7324 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 96 305 5683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0365544
X-RAY DIFFRACTIONf_angle_d3.1097556
X-RAY DIFFRACTIONf_dihedral_angle_d15.9121965
X-RAY DIFFRACTIONf_chiral_restr0.258780
X-RAY DIFFRACTIONf_plane_restr0.017962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0504-2.10580.4032720.39033320X-RAY DIFFRACTION53
2.1058-2.16780.34721090.33274412X-RAY DIFFRACTION70
2.1678-2.23770.34321200.27584977X-RAY DIFFRACTION79
2.2377-2.31770.28671380.24585218X-RAY DIFFRACTION83
2.3177-2.41050.28681290.22995523X-RAY DIFFRACTION87
2.4105-2.52020.2751280.22235571X-RAY DIFFRACTION88
2.5202-2.65310.29311440.2225780X-RAY DIFFRACTION91
2.6531-2.81930.25471460.21095906X-RAY DIFFRACTION93
2.8193-3.03690.21741450.20786121X-RAY DIFFRACTION96
3.0369-3.34250.22731530.20166186X-RAY DIFFRACTION97
3.3425-3.8260.20531560.176296X-RAY DIFFRACTION98
3.826-4.81970.18391560.15066382X-RAY DIFFRACTION99
4.8197-48.83360.17811570.16766590X-RAY DIFFRACTION100

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