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- PDB-7nc5: Glutathione-S-transferase GliG in complex with reduced glutathione -

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Basic information

Entry
Database: PDB / ID: 7nc5
TitleGlutathione-S-transferase GliG in complex with reduced glutathione
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 / glutathione transferase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)176,11920
Polymers173,7786
Non-polymers2,34014
Water14,718817
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7277
Polymers57,9262
Non-polymers8015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-10 kcal/mol
Surface area19580 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7898
Polymers57,9262
Non-polymers8636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-9 kcal/mol
Surface area19600 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6035
Polymers57,9262
Non-polymers6773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-24 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.570, 85.860, 345.870
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: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
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, 20 % PEG 3350

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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: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48 Å / Num. obs: 116899 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.6
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 16164

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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: 1.95→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.735 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 5843 5 %RANDOM
Rwork0.1686 ---
obs0.1705 111020 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90 Å2 / Biso mean: 36.834 Å2 / Biso min: 21.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å2-0 Å2
2---1.06 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11576 0 152 817 12545
Biso mean--49.25 45.21 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01312143
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711406
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.65116472
X-RAY DIFFRACTIONr_angle_other_deg1.0871.57626446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65951448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23221.233657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.383152107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2481593
X-RAY DIFFRACTIONr_chiral_restr0.0450.21531
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022621
X-RAY DIFFRACTIONr_rigid_bond_restr0.372323549
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 428 -
Rwork0.255 8133 -
all-8561 -
obs--99.84 %
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)
10.07030.00380.00190.0593-0.0180.09-0.002-0.01170.00130.00670.00070.00170.0013-0.00060.00120.0280.00050.00130.02480.00020.0045-17.152-3.77881.658
20.1233-0.01950.02150.0715-0.01820.08050.00150.0123-0.0015-0.00750.0004-0.00050.00130.0068-0.00190.0298-0.00060.00230.02330.00020.0032-15.701-5.17758.056
30.0540.00960.03620.2125-0.0740.0722-0.00250.0031-0.0042-0.00930.0003-0.01680.0049-0.00240.00220.02950.00060.00310.022-0.00310.0039-14.716-3.988115.441
40.0591-0.00440.00140.1199-0.06940.1320.0018-0.0047-0.00570.0307-0.0021-0.0077-0.023-0.00340.00030.0368-0.0021-0.00190.0206-0.00270.0019-14.3050.092138.74
50.09070.0401-0.06760.0967-0.01130.13110.00430.0017-0.0009-0.0183-0.00910.008-0.0146-0.00560.00480.03420.0041-0.00940.0214-0.00650.004-13.9431.558173.543
60.06030.0217-0.03730.0706-0.01380.17790.0114-0.0176-0.00460.0033-0.0180.0059-0.02840.00540.00660.0315-0.0036-0.00560.0282-0.00610.0038-10.6774.271196.798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 240
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B3 - 239
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION3C1 - 239
6X-RAY DIFFRACTION3C301
7X-RAY DIFFRACTION4D2 - 239
8X-RAY DIFFRACTION4D301
9X-RAY DIFFRACTION5E2 - 239
10X-RAY DIFFRACTION5E301
11X-RAY DIFFRACTION6F3 - 239
12X-RAY DIFFRACTION6F301

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