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- PDB-4g19: Crystal structure of the glutathione transferase GTE1 from Phaner... -

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Basic information

Entry
Database: PDB / ID: 4g19
TitleCrystal structure of the glutathione transferase GTE1 from Phanerochaete chrysosporium in complex with glutathione
ComponentsGlutathione transferase GTE1
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
ACETATE ION / GLUTATHIONE / Glutathione transferase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Glutathione transferase GTE1
B: Glutathione transferase GTE1
C: Glutathione transferase GTE1
D: Glutathione transferase GTE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,74421
Polymers115,5154
Non-polymers2,22817
Water11,638646
1
A: Glutathione transferase GTE1
B: Glutathione transferase GTE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,91811
Polymers57,7582
Non-polymers1,1609
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-18 kcal/mol
Surface area22250 Å2
MethodPISA
2
C: Glutathione transferase GTE1
D: Glutathione transferase GTE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,82610
Polymers57,7582
Non-polymers1,0688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-16 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.573, 88.146, 156.490
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 GTE1


Mass: 28878.857 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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7
Details: 30% PEG 8000, 200 mM sodium acetate and 100 mM HEPES., pH 7.0, MICROBATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97854 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2→48.48 Å / Num. all: 81606 / Num. obs: 81606 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20
Reflection shellResolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4.7 / Num. unique all: 11712 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Xnemodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F03

4f03


Resolution: 2→44.892 Å / SU ML: 0.49 / σ(F): 0 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 4087 5.01 %RANDOM
Rwork0.1766 ---
all0.1788 81510 --
obs0.1788 81510 99.95 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.144 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8957 Å2-0 Å2-0 Å2
2---5.2581 Å20 Å2
3----0.6377 Å2
Refinement stepCycle: LAST / Resolution: 2→44.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8112 0 146 646 8904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078558
X-RAY DIFFRACTIONf_angle_d1.02911616
X-RAY DIFFRACTIONf_dihedral_angle_d13.9723105
X-RAY DIFFRACTIONf_chiral_restr0.0711198
X-RAY DIFFRACTIONf_plane_restr0.0051474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02350.32511460.22582634X-RAY DIFFRACTION100
2.0235-2.04820.25541400.20912635X-RAY DIFFRACTION100
2.0482-2.07410.29071370.20122630X-RAY DIFFRACTION100
2.0741-2.10140.27261450.19522625X-RAY DIFFRACTION100
2.1014-2.13020.23041440.18962638X-RAY DIFFRACTION100
2.1302-2.16070.23011290.18632649X-RAY DIFFRACTION100
2.1607-2.19290.24981470.18492627X-RAY DIFFRACTION100
2.1929-2.22720.24651250.1822654X-RAY DIFFRACTION100
2.2272-2.26370.231190.18122689X-RAY DIFFRACTION100
2.2637-2.30270.26781430.18562621X-RAY DIFFRACTION100
2.3027-2.34460.22621510.18582637X-RAY DIFFRACTION100
2.3446-2.38970.24251530.17332616X-RAY DIFFRACTION100
2.3897-2.43840.22321340.17962664X-RAY DIFFRACTION100
2.4384-2.49150.22191360.1762666X-RAY DIFFRACTION100
2.4915-2.54940.23751530.17262627X-RAY DIFFRACTION100
2.5494-2.61320.21651160.17122695X-RAY DIFFRACTION100
2.6132-2.68380.2131390.16652651X-RAY DIFFRACTION100
2.6838-2.76280.21281530.17372639X-RAY DIFFRACTION100
2.7628-2.85190.25651390.17472688X-RAY DIFFRACTION100
2.8519-2.95380.22981510.17592657X-RAY DIFFRACTION100
2.9538-3.07210.22461530.17482651X-RAY DIFFRACTION100
3.0721-3.21190.20591450.1732662X-RAY DIFFRACTION100
3.2119-3.38120.19821190.16722714X-RAY DIFFRACTION100
3.3812-3.59290.20191490.17362677X-RAY DIFFRACTION100
3.5929-3.87020.23531380.1692702X-RAY DIFFRACTION100
3.8702-4.25940.18171410.16162717X-RAY DIFFRACTION100
4.2594-4.87510.17381470.1582731X-RAY DIFFRACTION100
4.8751-6.13960.19091480.17822754X-RAY DIFFRACTION100
6.1396-44.90290.24191470.19752873X-RAY DIFFRACTION99

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