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- PDB-5egp: Crystal structure of the S-methyltransferase TmtA -

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Basic information

Entry
Database: PDB / ID: 5egp
TitleCrystal structure of the S-methyltransferase TmtA
ComponentsUbiE/COQ5 family methyltransferase, putative
KeywordsTRANSFERASE / bis-thiomethyltransferase / gliotoxin / epipolythiodioxopiperazine / Aspergillus fumigatus
Function / homologyubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / UbiE/COQ5 family methyltransferase, putative
Function and homology information
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsDuell, E.R. / Glaser, M. / Antes, I. / Groll, M. / Huber, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
Hans-Fischer-Gesellschaft Germany
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Sequential Inactivation of Gliotoxin by the S-Methyltransferase TmtA.
Authors: Duell, E.R. / Glaser, M. / Le Chapelain, C. / Antes, I. / Groll, M. / Huber, E.M.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)72,59012
Polymers71,2752
Non-polymers1,31510
Water9,368520
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A: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2956
Polymers35,6371
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2956
Polymers35,6371
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.100, 109.210, 59.940
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UbiE/COQ5 family methyltransferase, putative


Mass: 35637.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_02735 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0J5Q3C4*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium acetate, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. obs: 89458 / % possible obs: 95.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.53 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.323 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16393 4473 5 %RANDOM
Rwork0.1324 ---
obs0.13397 84984 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0.18 Å2
2---0.56 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4449 0 86 520 5055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024659
X-RAY DIFFRACTIONr_bond_other_d0.0030.024397
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9756341
X-RAY DIFFRACTIONr_angle_other_deg0.9133.00510157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75425.248202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28115780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2421.1342270
X-RAY DIFFRACTIONr_mcbond_other1.2341.1292264
X-RAY DIFFRACTIONr_mcangle_it1.5721.7012825
X-RAY DIFFRACTIONr_mcangle_other1.5721.7012826
X-RAY DIFFRACTIONr_scbond_it1.8531.4922389
X-RAY DIFFRACTIONr_scbond_other1.8531.4932390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1542.0963513
X-RAY DIFFRACTIONr_long_range_B_refined3.11911.3025779
X-RAY DIFFRACTIONr_long_range_B_other3.11911.3055780
X-RAY DIFFRACTIONr_rigid_bond_restr1.88639056
X-RAY DIFFRACTIONr_sphericity_free26.7185162
X-RAY DIFFRACTIONr_sphericity_bonded7.00359306
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 322 -
Rwork0.277 6131 -
obs--94.59 %
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)
10.13520.07090.13530.4418-0.1720.384-0.01190.0195-0.01380.07460.0140.0026-0.05510.0177-0.00210.01750.00020.00520.0180.00050.01516.9337-10.25744.6115
20.1409-0.0378-0.17280.369-0.00830.2774-0.03450.00620.0217-0.02160.05480.01660.0537-0.0034-0.02030.0153-0.00610.0010.0210.00640.021113.138216.2366-12.5128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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