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- PDB-5jgl: Crystal structure of GtmA in complex with S-Adenosylmethionine -

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Basic information

Entry
Database: PDB / ID: 5jgl
TitleCrystal structure of GtmA in complex with S-Adenosylmethionine
ComponentsUbiE/COQ5 family methyltransferase, putative
KeywordsTRANSFERASE / Aspergillus fumigatus / Methyltransferase / S-Adenosylmethionine / Gliotoxin / Resistance
Function / homologyubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / UbiE/COQ5 family methyltransferase, putative
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDolan, S.K. / Bock, T. / Hering, V. / Jones, G.W. / Blankenfeldt, W. / Doyle, S.
CitationJournal: Open Biol / Year: 2017
Title: Structural, mechanistic and functional insight into gliotoxinbis-thiomethylation inAspergillus fumigatus.
Authors: Dolan, S.K. / Bock, T. / Hering, V. / Owens, R.A. / Jones, G.W. / Blankenfeldt, W. / Doyle, S.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: UbiE/COQ5 family methyltransferase, putative
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7556
Polymers64,9122
Non-polymers8434
Water93752
1
A: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8773
Polymers32,4561
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8773
Polymers32,4561
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.989, 114.142, 56.438
Angle α, β, γ (deg.)90.000, 104.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UbiE/COQ5 family methyltransferase, putative


Mass: 32455.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: Y699_02735 / Variant: ATCC 26933 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J5Q3C4
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M sodium phosphate citrate pH 4.2, 22% (w/v) PEG 8000, 0.08% (w/v) ellipticine, 0.20% (w/v) gibbeellin A3, 0.20% (w/v) trans-cinnamic acid, 0.20% (w/v) phenol, 0.20% (w/v) succinic acid ...Details: 0.1 M sodium phosphate citrate pH 4.2, 22% (w/v) PEG 8000, 0.08% (w/v) ellipticine, 0.20% (w/v) gibbeellin A3, 0.20% (w/v) trans-cinnamic acid, 0.20% (w/v) phenol, 0.20% (w/v) succinic acid disodium salt hexahydrate and 0.02 M HEPES pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.3855 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3855 Å / Relative weight: 1
ReflectionResolution: 2.28→49.275 Å / Num. obs: 50076 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 19.5 % / Biso Wilson estimate: 32.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.08
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.28-2.410.5752.78192.3
2.41-2.580.4194.31199.5
2.58-2.790.2786.18199.7
2.79-3.050.1819.35199.2
3.05-3.410.10515.49199.3
3.41-3.930.07323.06199.5
3.93-4.810.05131.68199.5
4.81-6.770.05330.93199.1
6.77-49.2750.03643.54199.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→49.275 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 26.37
RfactorNum. reflection% reflection
Rfree0.2336 2096 4.19 %
Rwork0.1915 --
obs0.1933 50072 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.69 Å2 / Biso mean: 44.7729 Å2 / Biso min: 18.14 Å2
Refinement stepCycle: final / Resolution: 2.28→49.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4163 0 96 52 4311
Biso mean--42.08 32.38 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034324
X-RAY DIFFRACTIONf_angle_d0.6215908
X-RAY DIFFRACTIONf_chiral_restr0.041681
X-RAY DIFFRACTIONf_plane_restr0.003746
X-RAY DIFFRACTIONf_dihedral_angle_d13.0882542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2763-2.32930.30821210.28392765288684
2.3293-2.38750.29321350.26313118325398
2.3875-2.45210.32661450.24563299344499
2.4521-2.52430.25111430.222232243367100
2.5243-2.60570.27551410.22723226336799
2.6057-2.69880.31241410.22893263340499
2.6988-2.80690.26121420.21931883330100
2.8069-2.93460.3011430.21983226336999
2.9346-3.08930.25241400.221632633403100
3.0893-3.28280.26251420.2153235337799
3.2828-3.53620.24471440.200232683412100
3.5362-3.8920.23711370.182131873324100
3.892-4.45480.17151370.14363245338299
4.4548-5.61140.14631440.142232363380100
5.6114-49.28670.22111410.16363233337499

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