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- PDB-7nc1: Glutathione-S-transferase GliG with partially disordered active site -

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Basic information

Entry
Database: PDB / ID: 7nc1
TitleGlutathione-S-transferase GliG with partially disordered active site
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
ACETATE ION / glutathione transferase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)57,9853
Polymers57,9262
Non-polymers591
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-12 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.760, 79.760, 119.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutathione S-transferase GliG


Mass: 28963.014 Da / Num. of mol.: 2
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.9 Å3/Da / Density % sol: 35.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.7, 32 % PEG2000MME

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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 PILATUS 6M-F / Detector: PIXEL / Date: Aug 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 14009 / % possible obs: 99.8 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.4
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1449

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→23.93 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 24.24 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 701 5 %RANDOM
Rwork0.2043 ---
obs0.2064 13308 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.34 Å2 / Biso mean: 51.587 Å2 / Biso min: 21.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å2-1.14 Å2-0 Å2
2---2.28 Å20 Å2
3---7.39 Å2
Refinement stepCycle: final / Resolution: 2.6→23.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 4 38 3421
Biso mean--58.07 41.15 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133494
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173278
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.6474739
X-RAY DIFFRACTIONr_angle_other_deg1.0951.5767586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89321.429196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95115610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5121530
X-RAY DIFFRACTIONr_chiral_restr0.0490.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
LS refinement shellResolution: 2.601→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 50 -
Rwork0.261 951 -
all-1001 -
obs--100 %
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)
12.2286-0.1829-0.83890.45520.25580.7758-0.2313-0.2183-0.03570.1930.1410.08850.06280.11540.09030.26220.09270.05320.11930.03530.0268-13.189322.344920.718
21.3796-0.2216-0.50510.7977-0.12980.7335-0.02640.1284-0.01520.0719-0.00830.1482-0.03610.04960.03470.1304-0.004-0.02770.11510.00230.0756-14.624.3425-4.1258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 238
2X-RAY DIFFRACTION2B2 - 240

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