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- PDB-7ncm: Glutathione-S-transferase GliG mutant E82A -

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Basic information

Entry
Database: PDB / ID: 7ncm
TitleGlutathione-S-transferase GliG mutant E82A
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
glutathione transferase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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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)57,8723
Polymers57,8102
Non-polymers621
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-13 kcal/mol
Surface area20070 Å2
Unit cell
Length a, b, c (Å)65.430, 80.450, 94.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutathione S-transferase GliG


Mass: 28904.979 Da / Num. of mol.: 2 / Mutation: E82A
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.3 M sodium/potassium tartrate, 21% PEG3350

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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: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 54425 / % possible obs: 98 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8584

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NC3

7nc3


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.495 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2721 5 %RANDOM
Rwork0.1719 ---
obs0.1742 51696 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.72 Å2 / Biso mean: 40.74 Å2 / Biso min: 24.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20 Å2
2---0.25 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3835 0 4 242 4081
Biso mean--31.8 44.96 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133975
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173737
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.655401
X-RAY DIFFRACTIONr_angle_other_deg1.2211.5758661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41421.469211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83115692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4381530
X-RAY DIFFRACTIONr_chiral_restr0.0630.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
X-RAY DIFFRACTIONr_rigid_bond_restr0.71237712
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 201 -
Rwork0.315 3819 -
all-4020 -
obs--99.46 %
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)
10.19590.06060.00880.4381-0.05030.38820.00780.04490.0184-0.03230.00120.048-0.0181-0.0526-0.00910.0770.0051-0.00290.0190.0030.037718.07116.59467.4407
20.2386-0.0006-0.02140.4716-0.01710.1070.0042-0.0560.03090.09970.00810.0172-0.01550.016-0.01230.1061-0.00280.00680.0146-0.00680.039423.98810.381429.8344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 239
2X-RAY DIFFRACTION2B2 - 238

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