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- PDB-7ncu: Glutathione-S-transferase GliG mutant K127G in complex with oxidi... -

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Basic information

Entry
Database: PDB / ID: 7ncu
TitleGlutathione-S-transferase GliG mutant K127G in complex with oxidized glutathione
ComponentsGlutathione S-transferase GliG
KeywordsBIOSYNTHETIC PROTEIN / Aspergillus fumigatus / mycotoxin / glutathione-S-transferase / carbon-sulphur-bond / epidithiodioxopiperazine
Function / homology
Function and homology information


glutathione transferase / molecular function activator activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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. / Soluble glutathione S-transferase N-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
OXIDIZED GLUTATHIONE DISULFIDE / glutathione transferase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGroll, M. / Huber, E.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural and Mechanistic Insights into C-S Bond Formation in Gliotoxin.
Authors: Scherlach, K. / Kuttenlochner, W. / Scharf, D.H. / Brakhage, A.A. / Hertweck, C. / Groll, M. / Huber, E.M.
History
DepositionJan 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 31, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,1316
Polymers57,7822
Non-polymers1,3494
Water11,259625
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-18 kcal/mol
Surface area19680 Å2
Unit cell
Length a, b, c (Å)126.260, 126.260, 64.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Glutathione S-transferase GliG


Mass: 28890.885 Da / Num. of mol.: 2 / Mutation: K127G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus A1163 (mold) / Gene: AFUB_075740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0Y813
#2: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE


Mass: 612.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N6O12S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M tris pH 8.5, 29 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. obs: 90330 / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.3
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16041

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NC3

7nc3


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.571 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 4516 5 %RANDOM
Rwork0.1431 ---
obs0.145 85802 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.67 Å2 / Biso mean: 27.234 Å2 / Biso min: 16.52 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å21 Å20 Å2
2--2 Å2-0 Å2
3----6.5 Å2
Refinement stepCycle: final / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 58 632 4550
Biso mean--35.32 43.58 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134090
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173824
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.6515558
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5758863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4521.187219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81115698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9551532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
X-RAY DIFFRACTIONr_rigid_bond_restr3.36337914
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 333 -
Rwork0.263 6318 -
all-6651 -
obs--95.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00850.00010.00970.0286-0.01570.0198-0.00110.00250.00060.0045-0.0007-0.0045-0.00350.00310.00180.00190.00080.00010.00190.00050.036441.8918-25.09220.6331
20.02250.02590.00160.0335-0.00090.0023-0.0030.0043-0.0014-0.00570.00490.00320.00210.0006-0.00190.00320-0.00020.0013-0.00130.037829.3832-31.9785-18.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 739
2X-RAY DIFFRACTION2B2 - 686

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