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- PDB-7ncl: Glutathione-S-transferase GliG mutant E82Q -

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Basic information

Entry
Database: PDB / ID: 7ncl
TitleGlutathione-S-transferase GliG mutant E82Q
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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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: 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 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)174,32217
Polymers173,7726
Non-polymers55011
Water10,773598
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2529
Polymers57,9242
Non-polymers3287
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-53 kcal/mol
Surface area19390 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1466
Polymers57,9242
Non-polymers2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-17 kcal/mol
Surface area19720 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,9242
Polymers57,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-17 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.330, 85.270, 346.250
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: 28962.029 Da / Num. of mol.: 6 / Mutation: E82Q
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
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, 23 % 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: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 104157 / % possible obs: 96.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3 / Num. unique obs: 14197

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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: 2→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.49 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 5207 5 %RANDOM
Rwork0.1749 ---
obs0.1772 98929 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.28 Å2 / Biso mean: 38.115 Å2 / Biso min: 22.25 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20 Å20 Å2
2---1.88 Å20 Å2
3----2.28 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11596 0 29 598 12223
Biso mean--43.55 44.66 -
Num. residues----1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01312046
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711320
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.65116356
X-RAY DIFFRACTIONr_angle_other_deg1.0941.57526248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73651451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06821.537644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.456152110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8571591
X-RAY DIFFRACTIONr_chiral_restr0.0450.21522
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022607
X-RAY DIFFRACTIONr_rigid_bond_restr0.426323366
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 388 -
Rwork0.24 7370 -
all-7758 -
obs--97.84 %
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)
10.0786-0.01940.0130.0896-0.02010.0753-0.0027-0.00620.00070.00790.00340.002-0.0003-0.0014-0.00070.00080.00020.00140.0153-0.0010.0151-17.2057-3.732381.7363
20.0897-0.01880.0270.0681-0.00420.06730.0030.0102-0.0009-0.0051-0.0016-0.0008-0.00130.0035-0.00140.0006-0.00020.00140.01510.00050.0153-15.4662-5.204458.1295
30.04360.01190.01120.1362-0.0470.07370.00040.0004-0.0045-0.0072-0.0006-0.0110.0044-0.00020.00020.00130.00040.00090.0135-0.00240.016-14.8414-4.0778115.5211
40.0475-0.0038-0.00660.1148-0.07350.14650.0021-0.0044-0.00210.0173-0.0036-0.0061-0.02040.00470.00150.0048-0.0045-0.00080.0121-0.0030.0129-14.50250.2415138.8561
50.0880.0148-0.01710.0450.00440.0531-0.00120.00280.0026-0.01130.0020.009-0.0097-0.0021-0.00080.0058-0.0006-0.00570.0147-0.00350.0125-13.99671.5389173.6741
60.07150.0022-0.03410.08250.0120.12430.0019-0.00690.00130.0023-0.00390.0006-0.0130.00060.0020.003-0.0026-0.0030.0132-0.00250.0128-10.78894.3266196.9979
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 240
2X-RAY DIFFRACTION2B3 - 239
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D2 - 239
5X-RAY DIFFRACTION5E1 - 239
6X-RAY DIFFRACTION6F2 - 239

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