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- PDB-7ncn: Glutathione-S-transferase GliG mutant S83A -

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Basic information

Entry
Database: PDB / ID: 7ncn
TitleGlutathione-S-transferase GliG mutant S83A
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, 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
Similarity search - Domain/homology
glutathione transferase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,93010
Polymers173,6826
Non-polymers2484
Water13,385743
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1426
Polymers57,8942
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint0 kcal/mol
Surface area19820 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,8942
Polymers57,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area20270 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,8942
Polymers57,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.110, 85.840, 347.800
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: 28947.014 Da / Num. of mol.: 6 / Mutation: S83A
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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5.5, 24 % 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: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 126946 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 18227

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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: 1.9→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.976 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 6346 5 %RANDOM
Rwork0.1825 ---
obs0.1843 120563 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.19 Å2 / Biso mean: 35.933 Å2 / Biso min: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å20 Å2-0 Å2
2---2.65 Å20 Å2
3----2.56 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11569 0 16 743 12328
Biso mean--40.73 43.17 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01312003
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711295
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.65116305
X-RAY DIFFRACTIONr_angle_other_deg1.0931.57526171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83251446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45321.413644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.519152095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7671593
X-RAY DIFFRACTIONr_chiral_restr0.0460.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022611
X-RAY DIFFRACTIONr_rigid_bond_restr0.489323298
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 473 -
Rwork0.294 8974 -
all-9447 -
obs--99.88 %
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)
10.0498-0.00610.00610.0585-0.01420.04220.0016-0.0028-0.00130.0047-0.00050.0023-0.00130.0001-0.00110.0005-00.00060.0481-0.00060.041-17.5067-4.062782.1213
20.0403-0.00830.01260.04250.00640.04920.00130.0069-0.0029-0.0045-0.001-0.0015-0.0009-0-0.00030.0005-0.00050.00080.0460.00090.0415-16.0092-5.37258.4235
30.0330.00760.0110.116-0.03430.05020.00070.0021-0.0038-0.0098-0.0018-0.00660.00360.00320.00110.00240.00050.00150.0474-0.00070.04-14.7059-4.2079116.2716
40.03920.0009-0.01620.1216-0.0590.1108-0.0018-0.00410.00150.0274-0.0011-0.0082-0.02490.00380.00280.0123-0.0017-0.00240.0447-0.00110.038-14.32680.2371139.5764
50.00870.00320.00970.04390.04640.0584-0.00190.00510.0038-0.0180.00020.0099-0.0181-0.00330.00170.0089-0.0005-0.00810.0469-0.00120.0422-13.811.6413174.5289
60.0394-0.0047-0.00430.07770.01840.09960.00100.0067-0.00140.0009-0.0007-0.0138-0.0077-0.00190.0027-0.0033-0.00290.0412-0.00320.041-10.45864.4734197.8723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 240
2X-RAY DIFFRACTION2B2 - 239
3X-RAY DIFFRACTION3C1 - 239
4X-RAY DIFFRACTION4D3 - 239
5X-RAY DIFFRACTION5E1 - 239
6X-RAY DIFFRACTION6F4 - 239

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