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- PDB-7nc8: Glutathione-S-transferase GliG mutant S24A -

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Basic information

Entry
Database: PDB / ID: 7nc8
TitleGlutathione-S-transferase GliG mutant S24A
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 / Soluble glutathione S-transferase N-terminal domain profile. / 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
Similarity search - Domain/homology
glutathione transferase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 28, 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)174,05412
Polymers173,6826
Non-polymers3726
Water7,891438
1
A: Glutathione S-transferase GliG
C: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0184
Polymers57,8942
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-6 kcal/mol
Surface area20300 Å2
MethodPISA
2
B: Glutathione S-transferase GliG
E: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0184
Polymers57,8942
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-10 kcal/mol
Surface area20170 Å2
MethodPISA
3
D: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0184
Polymers57,8942
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint1 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.810, 105.350, 207.080
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: S24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
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, 25 % 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: 2.2→49 Å / Num. obs: 89697 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 11149

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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: 2.2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.073 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 4483 5 %RANDOM
Rwork0.1902 ---
obs0.1926 85174 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.79 Å2 / Biso mean: 51.679 Å2 / Biso min: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å2-0 Å2-0 Å2
2--0.58 Å20 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11332 0 24 438 11794
Biso mean--47.18 51.1 -
Num. residues----1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311694
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711023
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.6515867
X-RAY DIFFRACTIONr_angle_other_deg1.0721.57525531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70851404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.721.449628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.386152042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4061591
X-RAY DIFFRACTIONr_chiral_restr0.0450.21483
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022531
X-RAY DIFFRACTIONr_rigid_bond_restr0.394322717
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 329 -
Rwork0.254 6247 -
all-6576 -
obs--99.82 %
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)
10.08650.03890.03730.0396-0.01820.24080.0024-0.00860.00620.0159-0.00310.00150.014-0.00380.00070.0782-0.0015-0.00190.0382-0.00280.0075-0.6475.8642-5.8385
20.1689-0.0142-0.02560.1589-0.0530.0835-0.0003-0.0257-0.0123-0.01280.01310.0018-0.00530.0031-0.01280.076-0.00290.00060.04460.0030.00841.154512.284628.1155
30.073-0.00640.05240.054-0.01150.17670.00860.0193-0.001-0.007-0.003-0.00220.01590.0114-0.00560.07790.0024-0.00180.0422-0.0030.0071.77734.6565-29.2891
40.091-0.0370.10180.208-0.20530.29030.0139-0.00260.0135-0.0169-0.0020.01580.0409-0.0007-0.01190.0799-0.0012-00.03980.0010.0066-38.858-5.350540.5424
50.1734-0.0254-0.06230.16340.03270.0657-0.0048-0.07850.01440.02330.0232-0.0108-0.01310.026-0.01840.0673-0.0041-0.00130.0702-0.0030.00562.213521.766749.8061
60.59670.6368-0.47511.202-0.34681.4767-0.0596-0.0472-0.06790.02720.0057-0.18040.3040.17610.05390.14240.0212-0.00820.0349-0.00160.0312-41.0301-10.031515.8732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 239
2X-RAY DIFFRACTION2B2 - 239
3X-RAY DIFFRACTION3C2 - 239
4X-RAY DIFFRACTION4D3 - 239
5X-RAY DIFFRACTION5E3 - 239
6X-RAY DIFFRACTION6F2 - 239

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