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- PDB-4f03: Crystal structure of the glutathione transferase GTE1 from Phaner... -

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Basic information

Entry
Database: PDB / ID: 4f03
TitleCrystal structure of the glutathione transferase GTE1 from Phanerochaete chrysosporium
ComponentsGlutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / GST fold / glutathione
Function / homology
Function and homology information


transferase activity
Similarity search - Function
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, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich ...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, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione transferase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDidierjean, C. / Favier, F. / Prosper, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Characterization of a Phanerochaete chrysosporium Glutathione Transferase Reveals a Novel Structural and Functional Class with Ligandin Properties.
Authors: Mathieu, Y. / Prosper, P. / Buee, M. / Dumarcay, S. / Favier, F. / Gelhaye, E. / Gerardin, P. / Harvengt, L. / Jacquot, J.P. / Lamant, T. / Meux, E. / Mathiot, S. / Didierjean, C. / Morel, M.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione transferase
B: Glutathione transferase
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,73911
Polymers116,0784
Non-polymers6617
Water16,286904
1
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3235
Polymers58,0392
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-18 kcal/mol
Surface area22350 Å2
MethodPISA
2
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4156
Polymers58,0392
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-15 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.989, 88.383, 157.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutathione transferase / Glutathione S-transferase


Mass: 29019.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: I6ZUH3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5
Details: 30% PEG 8000, 200mM sodium acetate, 100 mM sodium cacodylate, pH 6.5, MICROBATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2010
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→44.23 Å / Num. obs: 111495 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.2
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→42.539 Å / SU ML: 0.46 / σ(F): 0.07 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1983 1.78 %RANDOM
Rwork0.192 ---
all0.1926 111495 --
obs0.1926 111495 98.75 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.47 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.3041 Å2-0 Å2-0 Å2
2---4.3605 Å20 Å2
3----1.9436 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8112 0 38 904 9054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078402
X-RAY DIFFRACTIONf_angle_d1.02511411
X-RAY DIFFRACTIONf_dihedral_angle_d14.783038
X-RAY DIFFRACTIONf_chiral_restr0.0731183
X-RAY DIFFRACTIONf_plane_restr0.0041441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7984-1.84340.30011310.24937219X-RAY DIFFRACTION92
1.8434-1.89320.27381320.23017584X-RAY DIFFRACTION97
1.8932-1.94890.27531460.21587599X-RAY DIFFRACTION98
1.9489-2.01180.24181370.2087787X-RAY DIFFRACTION99
2.0118-2.08370.25221400.19857765X-RAY DIFFRACTION99
2.0837-2.16720.20331420.19597811X-RAY DIFFRACTION100
2.1672-2.26580.25421410.19147848X-RAY DIFFRACTION100
2.2658-2.38520.23841430.1937873X-RAY DIFFRACTION100
2.3852-2.53460.23111400.19487875X-RAY DIFFRACTION100
2.5346-2.73030.25861450.19527888X-RAY DIFFRACTION100
2.7303-3.0050.23031470.19167945X-RAY DIFFRACTION100
3.005-3.43970.22531430.1927959X-RAY DIFFRACTION100
3.4397-4.3330.2031470.17258037X-RAY DIFFRACTION100
4.333-42.55050.1941490.18358322X-RAY DIFFRACTION100

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