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- PDB-4fqu: Glutathionyl-Hydroquinone Reductase PcpF of Sphingobium chlorophe... -

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Basic information

Entry
Database: PDB / ID: 4fqu
TitleGlutathionyl-Hydroquinone Reductase PcpF of Sphingobium chlorophenolicum
ComponentsPutative glutathione transferase
KeywordsOXIDOREDUCTASE / Glutathionyl-Hydroquinone Reductases / TRANSFERASE
Function / homology
Function and homology information


glutathionyl-hydroquinone reductase / glutathione transferase activity / oxidoreductase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase Omega/GSH / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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 ...Glutathione S-transferase Omega/GSH / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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 PcpF
Similarity search - Component
Biological speciesSphingobium chlorophenolicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Jul 1, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative glutathione transferase
B: Putative glutathione transferase
C: Putative glutathione transferase
D: Putative glutathione transferase
E: Putative glutathione transferase
F: Putative glutathione transferase
G: Putative glutathione transferase
H: Putative glutathione transferase


Theoretical massNumber of molelcules
Total (without water)283,3838
Polymers283,3838
Non-polymers00
Water99155
1
A: Putative glutathione transferase
B: Putative glutathione transferase


Theoretical massNumber of molelcules
Total (without water)70,8462
Polymers70,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-11 kcal/mol
Surface area26350 Å2
MethodPISA
2
C: Putative glutathione transferase
D: Putative glutathione transferase


Theoretical massNumber of molelcules
Total (without water)70,8462
Polymers70,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area26360 Å2
MethodPISA
3
E: Putative glutathione transferase
F: Putative glutathione transferase


Theoretical massNumber of molelcules
Total (without water)70,8462
Polymers70,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-10 kcal/mol
Surface area26390 Å2
MethodPISA
4
G: Putative glutathione transferase

H: Putative glutathione transferase


Theoretical massNumber of molelcules
Total (without water)70,8462
Polymers70,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
Buried area2210 Å2
ΔGint-9 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.845, 242.845, 242.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
Putative glutathione transferase


Mass: 35422.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium chlorophenolicum (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8KN33
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1M MES monohydrate, 10% v/v 1,4-dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.6 Å / Num. all: 243097 / Num. obs: 162729 / % possible obs: 91.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.0001→3.0493 Å / % possible all: 72

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.571 Å / SU ML: 0.44 / σ(F): 0.12 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 2888 1.77 %RANDOM
Rwork0.2021 ---
obs0.203 162729 87.9 %-
all-243097 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.111 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→49.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19674 0 0 55 19729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01720225
X-RAY DIFFRACTIONf_angle_d1.8627544
X-RAY DIFFRACTIONf_dihedral_angle_d17.4897325
X-RAY DIFFRACTIONf_chiral_restr0.1142904
X-RAY DIFFRACTIONf_plane_restr0.0083613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.04930.361120.32156249X-RAY DIFFRACTION72
3.0493-3.10190.37341140.30366371X-RAY DIFFRACTION74
3.1019-3.15830.36291200.29636695X-RAY DIFFRACTION77
3.1583-3.2190.37141200.28316823X-RAY DIFFRACTION79
3.219-3.28470.33761290.26156969X-RAY DIFFRACTION80
3.2847-3.35610.26191380.24097050X-RAY DIFFRACTION82
3.3561-3.43420.27241110.23167339X-RAY DIFFRACTION84
3.4342-3.520.32131310.22747499X-RAY DIFFRACTION86
3.52-3.61520.2981350.20627587X-RAY DIFFRACTION87
3.6152-3.72150.2271400.19067525X-RAY DIFFRACTION87
3.7215-3.84160.24861410.18587655X-RAY DIFFRACTION89
3.8416-3.97890.20811350.17957899X-RAY DIFFRACTION91
3.9789-4.13810.22561530.16498013X-RAY DIFFRACTION92
4.1381-4.32630.23711450.16067928X-RAY DIFFRACTION92
4.3263-4.55430.19961450.14848187X-RAY DIFFRACTION94
4.5543-4.83940.20871460.15978210X-RAY DIFFRACTION95
4.8394-5.21270.24331530.15828202X-RAY DIFFRACTION95
5.2127-5.73650.23281500.15848284X-RAY DIFFRACTION95
5.7365-6.5650.23691510.17368348X-RAY DIFFRACTION96
6.565-8.2650.18731600.16168461X-RAY DIFFRACTION98
8.265-49.57730.24841590.18338547X-RAY DIFFRACTION99

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