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- PDB-7ncd: Glutathione-S-transferase GliG mutant N27D -

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Basic information

Entry
Database: PDB / ID: 7ncd
TitleGlutathione-S-transferase GliG mutant N27D
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 speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)174,15313
Polymers173,7846
Non-polymers3697
Water4,720262
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1116
Polymers57,9282
Non-polymers1834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-26 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0524
Polymers57,9282
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-10 kcal/mol
Surface area19940 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9903
Polymers57,9282
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-12 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.030, 85.030, 345.010
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: 28963.998 Da / Num. of mol.: 6 / Mutation: N27D
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 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: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→49 Å / Num. obs: 100404 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.8
Reflection shellResolution: 2.05→2.15 Å / Rmerge(I) obs: 0.538 / Num. unique obs: 13290

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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: 2.05→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 14.681 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 5019 5 %RANDOM
Rwork0.2096 ---
obs0.2111 95351 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.34 Å2 / Biso mean: 51.456 Å2 / Biso min: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å2-0 Å2
2---0.71 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11606 0 22 262 11890
Biso mean--41.35 50.41 -
Num. residues----1433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311972
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711256
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.65116247
X-RAY DIFFRACTIONr_angle_other_deg1.0951.57626085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7951437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78821.438640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.068152092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2911592
X-RAY DIFFRACTIONr_chiral_restr0.0450.21515
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022593
X-RAY DIFFRACTIONr_rigid_bond_restr0.357323228
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 368 -
Rwork0.307 6978 -
all-7346 -
obs--99.97 %
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)
10.95950.01190.0010.65880.05190.9628-0.0284-0.1475-0.04710.15870.01660.0695-0.00870.0170.01170.33660.00460.00350.2220.02860.2631-17.3346-4.359281.3445
21.1875-0.0891-0.00680.7445-0.06880.9552-0.03550.2796-0.0771-0.0850.04160.01430.02450.0705-0.00610.2799-0.0191-0.01050.2781-0.02190.2602-15.4903-5.703657.8675
30.54330.0090.24961.1666-0.60161.0479-0.08180.0894-0.0557-0.25470.0676-0.13870.1245-0.12560.01420.4437-0.0095-0.01890.2262-0.10240.1718-15.1671-4.6059115.5853
40.35480.16210.17030.6743-0.97342.0316-0.0651-0.0473-0.09490.14120.0639-0.1048-0.2856-0.15170.00120.43350.0328-0.02850.2134-0.07650.1695-14.7349-0.1178138.5747
50.96830.3092-0.56920.71780.16841.1595-0.0234-0.2461-0.0588-0.2075-0.15440.0194-0.2951-0.10960.17780.4190.0751-0.10670.3184-0.16280.1476-14.01212.0735172.8592
60.06040.069-0.17340.48810.49352.38520.0395-0.1747-0.01810.0099-0.29870.1039-0.53810.37470.25920.384-0.0695-0.08160.6667-0.07520.1151-10.91774.5723196.0273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 240
2X-RAY DIFFRACTION2B2 - 239
3X-RAY DIFFRACTION3C0 - 239
4X-RAY DIFFRACTION4D2 - 239
5X-RAY DIFFRACTION5E-1 - 239
6X-RAY DIFFRACTION6F3 - 239

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