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- PDB-7nc6: Glutathione-S-transferase GliG in complex with cyclo[L-Phe-L-Ser]... -

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Basic information

Entry
Database: PDB / ID: 7nc6
TitleGlutathione-S-transferase GliG in complex with cyclo[L-Phe-L-Ser]-bis-glutathione-adduct
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
ACETATE ION / Chem-U8B / glutathione transferase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)177,45316
Polymers173,7786
Non-polymers3,67510
Water4,864270
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2527
Polymers57,9262
Non-polymers1,3265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1315
Polymers57,9262
Non-polymers1,2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-21 kcal/mol
Surface area19590 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0694
Polymers57,9262
Non-polymers1,1432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-16 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.370, 85.300, 344.800
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.) Aspergillus fumigatus A1163 (mold) / Gene: AFUB_075740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0Y813
#2: Chemical
ChemComp-U8B / (2~{S})-2-azanyl-5-[[(2~{R})-3-[(2~{R},5~{R})-5-(hydroxymethyl)-3,6-bis(oxidanylidene)-2-(phenylmethyl)-5-sulfanyl-piperazin-2-yl]sulfanyl-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid


Mass: 571.624 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H29N5O9S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.53 %
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: 2.1→48 Å / Num. obs: 92409 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 11933

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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: 2.1→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 17 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 4619 5 %RANDOM
Rwork0.1832 ---
obs0.1859 87753 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.98 Å2 / Biso mean: 48.54 Å2 / Biso min: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å2-0 Å2-0 Å2
2--1.74 Å2-0 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11569 0 208 270 12047
Biso mean--70.29 51.44 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312082
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711299
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.6716406
X-RAY DIFFRACTIONr_angle_other_deg1.1961.59626185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92651422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04221.523637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.082152071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0191590
X-RAY DIFFRACTIONr_chiral_restr0.0510.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022607
X-RAY DIFFRACTIONr_rigid_bond_restr0.819323379
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 338 -
Rwork0.261 6416 -
all-6754 -
obs--99.82 %
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)
10.15520.0216-0.050.0205-0.03150.1047-0.00620.014-0.0025-0.0041-0.0062-0.00260.00610.00490.01240.13920.00090.00210.0570.00310.0136-16.089-5.64757.621
20.13120.0163-0.07290.0144-0.02790.1495-0.0043-0.0296-0.0010.0006-0.00920.0090.00590.0180.01360.1357-0.00120.00050.05880.00230.0172-17.203-4.62981.19
30.0420.03110.02480.1666-0.01980.1064-0.00370.0048-0.0002-0.00680.0011-0.01690.004-0.01120.00260.1335-0.00180.00450.055-0.0090.0181-14.38-4.364115.207
40.0332-0.0031-0.0130.0832-0.02680.1212-0.0039-0.00540.0030.01530.0033-0.0192-0.0077-0.00990.00070.1366-0.0007-0.00130.0558-0.00810.0163-14.1480.044138.389
50.03510.0433-0.02450.08670.02590.197-0.0036-0.0160.0032-0.0189-0.01760.0101-0.0214-0.01210.02120.14070.0085-0.00960.056-0.01550.0152-13.3651.706172.831
60.05870.0107-0.03240.1470.03410.22310.005-0.05830.0136-0.0015-0.02260.0115-0.02110.01270.01760.14160.001-0.00490.0757-0.01790.0066-10.1214.272196.095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 239
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B2 - 239
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION3C1 - 239
6X-RAY DIFFRACTION3C301
7X-RAY DIFFRACTION4D3 - 239
8X-RAY DIFFRACTION4D301
9X-RAY DIFFRACTION5E2 - 239
10X-RAY DIFFRACTION5E301
11X-RAY DIFFRACTION6F3 - 239
12X-RAY DIFFRACTION6F301

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