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- PDB-7nc9: Glutathione-S-transferase GliG mutant H26N -

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Basic information

Entry
Database: PDB / ID: 7nc9
TitleGlutathione-S-transferase GliG mutant H26N
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
glutathione transferase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)173,7588
Polymers173,6346
Non-polymers1242
Water1,33374
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9403
Polymers57,8782
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-15 kcal/mol
Surface area19930 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG


Theoretical massNumber of molelcules
Total (without water)57,8782
Polymers57,8782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-17 kcal/mol
Surface area19990 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9403
Polymers57,8782
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-13 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)267.820, 86.180, 63.640
Angle α, β, γ (deg.)90.000, 92.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glutathione S-transferase GliG


Mass: 28938.971 Da / Num. of mol.: 6 / Mutation: H26N
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5, 26 %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: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→47 Å / Num. obs: 45771 / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 2.55→2.65 Å / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4934

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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: 2.55→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 32.749 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 2287 5 %RANDOM
Rwork0.2282 ---
obs0.2299 43459 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.59 Å2 / Biso mean: 64.186 Å2 / Biso min: 37.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å21.34 Å2
2--3.28 Å20 Å2
3----2.5 Å2
Refinement stepCycle: final / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11490 0 8 74 11572
Biso mean--60.5 54.46 -
Num. residues----1418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01311799
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711102
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.65116020
X-RAY DIFFRACTIONr_angle_other_deg1.0571.57525725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85851414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65921.564633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.032152057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2241590
X-RAY DIFFRACTIONr_chiral_restr0.0420.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022548
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 165 -
Rwork0.371 3128 -
all-3293 -
obs--95.98 %
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)
10.95310.4946-0.58590.3186-0.46530.93170.0442-0.3230.1314-0.0298-0.11590.06590.1026-0.04270.07170.0541-0.062-0.00320.2177-0.1380.1721-32.416631.726357.0662
21.18930.5204-0.52990.2898-0.36580.7167-0.0199-0.02430.1992-0.0572-0.03680.04170.03150.0670.05670.1172-0.0088-0.02040.0482-0.04860.2856-17.311541.742642.0275
31.87860.4451-0.62010.1231-0.1111.1890.00820.40770.03560.05560.0643-0.00360.1719-0.0402-0.07250.1611-0.0503-0.02340.2152-0.01010.042-61.6479-20.210740.3259
41.4428-0.0628-0.45910.0397-0.04730.5611-0.0029-0.18240.0231-0.02370.08160.03640.0097-0.0368-0.07870.1003-0.01040.01110.23140.03820.0849-80.0781-20.980354.8969
50.73110.375-0.61270.4051-0.15711.0444-0.0297-0.06830.01580.02430.0327-0.11150.0545-0.2195-0.0030.10920.0051-0.06820.2667-0.08680.0995-33.7369-10.617625.566
60.81460.3334-0.2570.5173-0.36790.5845-0.11230.04610.0552-0.08740.1121-0.1685-0.0352-0.00780.00020.1541-0.0066-0.04330.0512-0.09720.2209-18.6661-1.020210.3468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 238
2X-RAY DIFFRACTION2B3 - 239
3X-RAY DIFFRACTION3C3 - 238
4X-RAY DIFFRACTION4D3 - 238
5X-RAY DIFFRACTION5E3 - 238
6X-RAY DIFFRACTION6F3 - 239

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