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- PDB-5jgj: Crystal structure of GtmA -

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Basic information

Entry
Database: PDB / ID: 5jgj
TitleCrystal structure of GtmA
ComponentsUbiE/COQ5 family methyltransferase, putative
KeywordsTRANSFERASE / Aspergillus fumigatus / Methyltransferase / Gliotoxin / Resistance
Function / homologyubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / Vaccinia Virus protein VP39 / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / UbiE/COQ5 family methyltransferase, putative
Function and homology information
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 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: PDBE / 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UbiE/COQ5 family methyltransferase, putative


Theoretical massNumber of molelcules
Total (without water)32,4561
Polymers32,4561
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.729, 94.729, 52.729
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein UbiE/COQ5 family methyltransferase, putative


Mass: 32455.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_02735 / Variant: ATCC 26933 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J5Q3C4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.66→44.36 Å / Num. obs: 32033 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.012 / Rrim(I) all: 0.052 / Net I/σ(I): 29.7 / Num. measured all: 629629 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.66-1.6918.71.4692988115980.7650.3471.512.3100
9.09-44.3618.50.04639472130.9980.0110.04880.599.4

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Processing

Software
NameVersionClassification
PHENIXdev_2608refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→44.357 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 1564 4.89 %
Rwork0.1677 30446 -
obs0.1686 32010 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.58 Å2 / Biso mean: 63.6431 Å2 / Biso min: 24.54 Å2
Refinement stepCycle: final / Resolution: 1.66→44.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 0 131 1937
Biso mean---51.64 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171861
X-RAY DIFFRACTIONf_angle_d1.3522546
X-RAY DIFFRACTIONf_chiral_restr0.079292
X-RAY DIFFRACTIONf_plane_restr0.01327
X-RAY DIFFRACTIONf_dihedral_angle_d13.9231100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6602-1.71370.23761420.24527372879
1.7137-1.7750.22771700.223527452915
1.775-1.84610.21011060.204727642870
1.8461-1.93010.22371300.187827792909
1.9301-2.03180.19061560.182727392895
2.0318-2.15910.18951380.180627602898
2.1591-2.32580.18521560.169627412897
2.3258-2.55990.18281410.169427722913
2.5599-2.93020.20111680.171827572925
2.9302-3.69150.18671000.172128132913
3.6915-44.37270.17271570.15128392996
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)
15.0272.2389-0.86025.2466-0.52657.07810.2831-0.1809-0.37170.2701-0.08160.05640.6972-0.3697-0.22120.3086-0.1072-0.05790.29670.01450.304978.539443.79213.9578
24.10520.09631.94024.8882-0.32455.14840.175-0.35590.26460.2662-0.21520.2601-0.1723-0.7054-0.00340.2059-0.02860.03650.3877-0.00850.378.49156.457.0462
33.29780.56571.7772.7017-0.63192.2265-0.26270.39060.6517-0.63790.13170.6793-0.0989-0.22920.07460.36840.0205-0.14540.37990.09050.515172.095765.6135-9.316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 121 )A23 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 160 )A122 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 287 )A161 - 287

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