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- PDB-3ppu: Crystal structure of the glutathione-S-transferase Xi from Phaner... -

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Basic information

Entry
Database: PDB / ID: 3ppu
TitleCrystal structure of the glutathione-S-transferase Xi from Phanerochaete chrysosporium
ComponentsGlutathione-S-transferase
KeywordsTRANSFERASE / GST fold
Function / homology
Function and homology information


glutathione transferase activity
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, C-terminal domain superfamily ...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 / Glutathione-S-transferase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDidierjean, C. / Prosper, P. / Favier, F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Glutathione transferases of Phanerochaete chrysosporium: S-glutathionyl-p-hydroquinone reductase belongs to a new structural class.
Authors: Meux, E. / Prosper, P. / Ngadin, A. / Didierjean, C. / Morel, M. / Dumarcay, S. / Lamant, T. / Jacquot, J.P. / Favier, F. / Gelhaye, E.
History
DepositionNov 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione-S-transferase
B: Glutathione-S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4693
Polymers81,1622
Non-polymers3071
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-18 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.823, 70.331, 72.566
Angle α, β, γ (deg.)90.00, 98.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutathione-S-transferase


Mass: 40580.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Gene: GTO1 / Production host: Escherichia coli (E. coli) / References: UniProt: B3VQJ7
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8.5
Details: 20 to 30 % polyethylene glycol 4000 (PEG 4000), 0 to 0.2 M magnesium or calcium chloride and 0.1 M Tris-HCl, pH 8.5, Microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980547 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2008
RadiationMonochromator: 111 Silicon single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980547 Å / Relative weight: 1
ReflectionResolution: 2.3→46.66 Å / Num. obs: 36622 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 / Net I/σ(I): 19.8
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.8 / % possible all: 96

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Processing

Software
NameVersionClassification
Xnemodata collection
SHELXmodel building
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→46.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.872 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.208 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1831 5 %RANDOM
Rwork0.19059 ---
all0.19245 36622 --
obs0.19245 36622 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.671 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å21.45 Å2
2--4.29 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 20 221 5251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225201
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9457085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62523.488258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6571534
X-RAY DIFFRACTIONr_chiral_restr0.0880.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214058
X-RAY DIFFRACTIONr_mcbond_it0.6581.53076
X-RAY DIFFRACTIONr_mcangle_it1.24125014
X-RAY DIFFRACTIONr_scbond_it1.79332125
X-RAY DIFFRACTIONr_scangle_it2.8194.52068
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 113 -
Rwork0.259 2410 -
obs--93.58 %

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