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- PDB-7nct: Glutathione-S-transferase GliG mutant K127G -

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Basic information

Entry
Database: PDB / ID: 7nct
TitleGlutathione-S-transferase GliG mutant K127G
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 speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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


Theoretical massNumber of molelcules
Total (without water)173,3456
Polymers173,3456
Non-polymers00
Water88349
1
A: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,7822
Polymers57,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,7822
Polymers57,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutathione S-transferase GliG

E: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,7822
Polymers57,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_446-x-1/2,y-1/2,-z+11
4
E: Glutathione S-transferase GliG

C: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,7822
Polymers57,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456-x-1/2,y+1/2,-z+11
Unit cell
Length a, b, c (Å)139.430, 81.230, 126.980
Angle α, β, γ (deg.)90.000, 90.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glutathione S-transferase GliG


Mass: 28890.885 Da / Num. of mol.: 6 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30 % PEG 2000 MME

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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: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→47 Å / Num. obs: 39163 / % possible obs: 94.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 2.65→2.75 Å / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 4137

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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: 2.65→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 66.013 / SU ML: 0.533 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1957 5 %RANDOM
Rwork0.2143 ---
obs0.2176 37179 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 213.12 Å2 / Biso mean: 98.172 Å2 / Biso min: 47.11 Å2
Baniso -1Baniso -2Baniso -3
1--8.11 Å2-0 Å2-1 Å2
2---4.2 Å2-0 Å2
3---12.34 Å2
Refinement stepCycle: final / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11496 0 0 49 11545
Biso mean---119.81 -
Num. residues----1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311802
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711060
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.64916030
X-RAY DIFFRACTIONr_angle_other_deg1.0581.57525622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72851416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31521.483634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.937152038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9591590
X-RAY DIFFRACTIONr_chiral_restr0.040.21494
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022562
X-RAY DIFFRACTIONr_rigid_bond_restr0.659322857
LS refinement shellResolution: 2.65→2.718 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 146 -
Rwork0.378 2774 -
all-2920 -
obs--96.18 %
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)
12.21690.3158-0.21522.4178-0.77150.55770.1971-0.08570.11420.2417-0.1549-0.07420.04730.0204-0.04220.3179-0.0642-0.05040.4669-0.00960.0911-23.6746-37.232725.6264
22.48390.3805-0.09422.6136-0.38980.25840.060.3284-0.02230.00470.0771-0.0317-0.0576-0.0458-0.13710.2756-0.0487-0.02330.4101-0.00380.2237-68.263-40.779616.7536
31.67950.3131-0.61232.7778-0.01370.512-0.18880.1639-0.13290.060.14570.198-0.04930.14480.0430.32710.0209-0.04280.50750.03140.0694-26.108-40.549358.9866
41.83940.2268-0.03723.0306-0.86360.4561-0.15080.56990.0599-0.19430.1552-0.24450.2202-0.0447-0.00440.3115-0.04430.00920.6476-0.03980.0735-20.7076-37.59722.239
52.3809-0.463-0.75112.1142-0.16970.7946-0.15560.1301-0.2654-0.5669-0.0026-0.0237-0.091-0.18970.15820.5753-0.1062-0.01840.4268-0.0670.0517-47.0574-1.594944.492
62.154-0.42530.22832.7269-0.7550.43540.2953-0.27570.24420.6925-0.11890.0186-0.15410.0169-0.17650.4811-0.13540.01310.38-0.08380.1902-68.0168-37.427140.0024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 239
2X-RAY DIFFRACTION2B3 - 239
3X-RAY DIFFRACTION3C4 - 239
4X-RAY DIFFRACTION4D2 - 239
5X-RAY DIFFRACTION5E3 - 239
6X-RAY DIFFRACTION6F3 - 238

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