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- PDB-5lkd: Crystal structure of the Xi glutathione transferase ECM4 from Sac... -

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Basic information

Entry
Database: PDB / ID: 5lkd
TitleCrystal structure of the Xi glutathione transferase ECM4 from Saccharomyces cerevisiae in complex with glutathione
ComponentsGlutathione S-transferase omega-like 2
KeywordsTRANSFERASE / Saccharomyces cerevisiae / glutathione transferase / glutathione / quinone / ECM4 / YKR076W / Glutathionyl-hydroquinone reductase
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) activity / glutathione dehydrogenase (ascorbate) / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cell wall organization / 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 / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase omega-like 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSchwartz, M. / Didierjean, C. / Hecker, A. / Girardet, J.M. / Morel-Rouhier, M. / Gelhaye, E. / Favier, F.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones.
Authors: Schwartz, M. / Didierjean, C. / Hecker, A. / Girardet, J.M. / Morel-Rouhier, M. / Gelhaye, E. / Favier, F.
History
DepositionJul 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase omega-like 2
B: Glutathione S-transferase omega-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4284
Polymers88,8132
Non-polymers6152
Water11,494638
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-24 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.440, 82.440, 80.580
Angle α, β, γ (deg.)90.00, 95.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase omega-like 2 / Extracellular mutant protein 4 / Glutathione-dependent dehydroascorbate reductase


Mass: 44406.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ECM4, GTO2, YKR076W / Production host: Escherichia coli (E. coli)
References: UniProt: P36156, glutathione transferase, glutathione dehydrogenase (ascorbate)
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 277 K / Method: microbatch / Details: 20% (w/v) PEG 2000 MME, 0.1 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979767 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979767 Å / Relative weight: 1
ReflectionResolution: 1.68→47.59 Å / Num. obs: 78066 / % possible obs: 95 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.9
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.76 / % possible all: 74.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PPU

3ppu


Resolution: 1.68→47.582 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65
RfactorNum. reflection% reflection
Rfree0.2003 3899 5 %
Rwork0.1589 --
obs0.161 78008 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→47.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5733 0 40 638 6411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195938
X-RAY DIFFRACTIONf_angle_d1.4568052
X-RAY DIFFRACTIONf_dihedral_angle_d13.8033462
X-RAY DIFFRACTIONf_chiral_restr0.085852
X-RAY DIFFRACTIONf_plane_restr0.0121025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6804-1.70090.3071990.28711871X-RAY DIFFRACTION69
1.7009-1.72240.34031160.26822210X-RAY DIFFRACTION79
1.7224-1.7450.33681360.26872573X-RAY DIFFRACTION93
1.745-1.7690.3231380.24862624X-RAY DIFFRACTION95
1.769-1.79420.29051420.22862705X-RAY DIFFRACTION96
1.7942-1.8210.26411370.21632602X-RAY DIFFRACTION96
1.821-1.84950.25311410.21132678X-RAY DIFFRACTION96
1.8495-1.87980.24831410.20082660X-RAY DIFFRACTION96
1.8798-1.91220.24851420.19252702X-RAY DIFFRACTION96
1.9122-1.9470.23541390.18712644X-RAY DIFFRACTION96
1.947-1.98440.21171410.18272692X-RAY DIFFRACTION96
1.9844-2.02490.24061400.17942659X-RAY DIFFRACTION96
2.0249-2.0690.23331420.17322706X-RAY DIFFRACTION97
2.069-2.11710.23761400.16242676X-RAY DIFFRACTION96
2.1171-2.170.20121420.16412689X-RAY DIFFRACTION97
2.17-2.22870.20541430.16282713X-RAY DIFFRACTION97
2.2287-2.29430.21391410.15252686X-RAY DIFFRACTION97
2.2943-2.36830.18891410.15072675X-RAY DIFFRACTION97
2.3683-2.4530.20641420.1392707X-RAY DIFFRACTION97
2.453-2.55120.1751430.14372709X-RAY DIFFRACTION97
2.5512-2.66730.2011440.14742735X-RAY DIFFRACTION98
2.6673-2.80790.20751430.15562713X-RAY DIFFRACTION98
2.8079-2.98380.1861440.15352736X-RAY DIFFRACTION98
2.9838-3.21410.21421440.15192746X-RAY DIFFRACTION98
3.2141-3.53750.18211450.14672751X-RAY DIFFRACTION98
3.5375-4.04910.15741440.12842735X-RAY DIFFRACTION98
4.0491-5.10050.13851440.11962732X-RAY DIFFRACTION96
5.1005-47.60140.19031450.16472780X-RAY DIFFRACTION97

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