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- PDB-7nc3: Glutathione-S-transferase GliG (space group P212121) -

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Basic information

Entry
Database: PDB / ID: 7nc3
TitleGlutathione-S-transferase GliG (space group P212121)
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 speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 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


Theoretical massNumber of molelcules
Total (without water)173,7786
Polymers173,7786
Non-polymers00
Water15,961886
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,9262
Polymers57,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area19960 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,9262
Polymers57,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-19 kcal/mol
Surface area20270 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,9262
Polymers57,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-17 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 85.730, 347.670
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: 28963.014 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
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: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→49 Å / Num. obs: 191960 / % possible obs: 98.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.6
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 31117

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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: 7NC2

7nc2


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.176 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 9596 5 %RANDOM
Rwork0.1657 ---
obs0.1672 182331 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.7 Å2 / Biso mean: 30.371 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--2.01 Å2-0 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11555 0 0 886 12441
Biso mean---39.63 -
Num. residues----1425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01311910
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711192
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.6516178
X-RAY DIFFRACTIONr_angle_other_deg1.1921.57525944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04251431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69221.509636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.206152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7761590
X-RAY DIFFRACTIONr_chiral_restr0.0570.21511
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022577
X-RAY DIFFRACTIONr_rigid_bond_restr0.499323102
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 708 -
Rwork0.266 13459 -
all-14167 -
obs--99.42 %
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)
10.0106-0.0017-0.0030.0028-0.00150.012-0.0005-0.00280.00090.00020.0010.00040.001-0-0.00050.0422-0-0.00020.0023-0.00010.0315-17.4973-3.75682.0502
20.0174-0.00070.00450.0109-0.0030.0098-0.00010.00080.0007-0.0010.00030.0005-0.00050.0013-0.00030.04220.00050.00020.0031-0.00030.0307-15.7894-5.181858.4505
30.00490.0058-0.00280.0403-0.00880.00770.0001-0.0005-0.0006-0.0018-0.0003-0.00330.0009-0.00130.00020.0412-0.00010.00010.0015-00.0314-14.8674-4.052116.1747
40.00730.0008-0.01160.0326-0.01530.02810.0013-0.0016-0.00110.0058-0.0005-0.0022-0.00480.0014-0.00070.0416-0.0005-0.00080.001-0.00020.031-14.46680.2611139.4975
50.01280.00380.00030.011-0.01190.0294-0.00050.00090.0002-0.0030.00130.0018-0.00080.0009-0.00080.043-0.0003-0.00010.000500.031-14.03781.5134174.4973
60.0197-0.003-0.00920.0081-0.00720.01440.0007-0.0011-0.00030.0016-0.00050-0.00090.0023-0.00030.0424-0.0013-0.00050.0029-0.00050.0307-10.68794.4072197.8129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 239
2X-RAY DIFFRACTION2B3 - 239
3X-RAY DIFFRACTION3C1 - 239
4X-RAY DIFFRACTION4D3 - 239
5X-RAY DIFFRACTION5E2 - 239
6X-RAY DIFFRACTION6F4 - 239

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